flip strand of GappedAlignmentPairs Object
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Stefanie ▴ 360
@stefanie-5192
Last seen 10.2 years ago
Dear list, Let's say I have single-end strand-specific RNA-Seq data. Then I could read in the data with: library(GenomicRanges) > reads = readGappedAlignments("data.bam") As I typically don't know which strand has been sequenced, it might be necessary to flip the strand of the reads before doing any kind of summarizeOverlap: > strand(reads) = ifelse(strand(reads) == "+", "-", "+") Now I could do a 'summarizeOverlaps' between the reads and any kind of transcript database. Now, if I have paired-end strand-specific RNA-Seq data. I read the data: > reads = readGappedAlignmentPairs("data.bam") How can I flip the strand of the reads? As it's now paired-end data, it does not work as above. I could imagine several work-arounds, I just wonder if there is any straight approach which I miss at the moment.. best regards, Stefanie [[alternative HTML version deleted]]
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@valerie-obenchain-4275
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Hi Stephanie, A GappedAlignmentPairs object is made up of a 'left' and a 'right' GappedAlignments. > ex1_file <- system.file("extdata", "ex1.bam", package="Rsamtools") > galp <- readGappedAlignmentPairs(ex1_file, use.names=TRUE) You can extract the left/right parts with an accessor then look at strand, cigars, gaps etc. > left <- left(galp) > class(left) [1] "GappedAlignments" attr(,"package") [1] "GenomicRanges" > strand(left) factor-Rle of length 1572 with 665 runs Lengths: 3 25 1 1 1 3 1 1 3 2 2 ... 1 6 1 2 3 2 1 5 1 51 Values : - + - + - + - + - + - ... + - + - + - + - + - Levels(3): + - * > head(cigar(left)) [1] "35M" "36M" "35M" "36M" "35M" "35M" > head(ngap(left)) [1] 0 0 0 0 0 0 It's on these left/right pairs that you can reset the strand. > strand(left)[1:3] factor-Rle of length 3 with 1 run Lengths: 3 Values : + Levels(3): + - * > strand(left)[1:3] <- "-" > strand(left)[1:3] factor-Rle of length 3 with 1 run Lengths: 3 Values : - Levels(3): + - * Please be sure to read the details on the man page regarding how the strands were assigned. ?GappedAlignmentPairs Valerie On 02/27/13 05:55, Stefanie Tauber wrote: > Dear list, > > Let's say I have single-end strand-specific RNA-Seq data. > Then I could read in the data with: > > library(GenomicRanges) > >> reads = readGappedAlignments("data.bam") > As I typically don't know which strand has been sequenced, it might be necessary to flip the strand of the reads before doing any kind > of summarizeOverlap: > >> strand(reads) = ifelse(strand(reads) == "+", "-", "+") > Now I could do a 'summarizeOverlaps' between the reads and any kind of transcript database. > > Now, if I have paired-end strand-specific RNA-Seq data. > I read the data: >> reads = readGappedAlignmentPairs("data.bam") > How can I flip the strand of the reads? As it's now paired-end data, it does not work as above. > I could imagine several work-arounds, I just wonder if there is any straight approach which I miss at the moment.. > > > best regards, > Stefanie > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Hi Valerie, thanks for the quick answer. I have already checked how the strand is assigned for paired-end data. After setting the strand for the left and right parts, can I somehow rebuild the gappedalignmentPairs object? best, Stefanie Am 27.02.2013 um 16:06 schrieb Valerie Obenchain <vobencha@fhcrc.org>: > Hi Stephanie, > > A GappedAlignmentPairs object is made up of a 'left' and a 'right' GappedAlignments. > > > ex1_file <- system.file("extdata", "ex1.bam", package="Rsamtools") > > galp <- readGappedAlignmentPairs(ex1_file, use.names=TRUE) > > You can extract the left/right parts with an accessor then look at strand, cigars, gaps etc. > > > left <- left(galp) > > class(left) > [1] "GappedAlignments" > attr(,"package") > [1] "GenomicRanges" > > > strand(left) > factor-Rle of length 1572 with 665 runs > Lengths: 3 25 1 1 1 3 1 1 3 2 2 ... 1 6 1 2 3 2 1 5 1 51 > Values : - + - + - + - + - + - ... + - + - + - + - + - > Levels(3): + - * > > > head(cigar(left)) > [1] "35M" "36M" "35M" "36M" "35M" "35M" > > > head(ngap(left)) > [1] 0 0 0 0 0 0 > > It's on these left/right pairs that you can reset the strand. > > > strand(left)[1:3] > factor-Rle of length 3 with 1 run > Lengths: 3 > Values : + > Levels(3): + - * > > strand(left)[1:3] <- "-" > > strand(left)[1:3] > factor-Rle of length 3 with 1 run > Lengths: 3 > Values : - > Levels(3): + - * > > Please be sure to read the details on the man page regarding how the strands were assigned. > > ?GappedAlignmentPairs > > > Valerie > > On 02/27/13 05:55, Stefanie Tauber wrote: >> Dear list, >> >> Let's say I have single-end strand-specific RNA-Seq data. >> Then I could read in the data with: >> >> library(GenomicRanges) >> >>> reads = readGappedAlignments("data.bam") >> As I typically don't know which strand has been sequenced, it might be necessary to flip the strand of the reads before doing any kind >> of summarizeOverlap: >> >>> strand(reads) = ifelse(strand(reads) == "+", "-", "+") >> Now I could do a 'summarizeOverlaps' between the reads and any kind of transcript database. >> >> Now, if I have paired-end strand-specific RNA-Seq data. >> I read the data: >>> reads = readGappedAlignmentPairs("data.bam") >> How can I flip the strand of the reads? As it's now paired-end data, it does not work as above. >> I could imagine several work-arounds, I just wonder if there is any straight approach which I miss at the moment.. >> >> >> best regards, >> Stefanie >> >> >> >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > DI Stefanie Tauber Center for Integrative Bioinformatics Vienna (CIBIV) (CIBIV is a joint institute of Vienna University and Medical University) Max F. Perutz Laboratories (MFPL) Campus Vienna Biocenter 5 (VBC5), Ebene 1, Room 1812.2 Dr. Bohr Gasse 9 A-1030 Wien, Austria Phone: ++43 +1 / 42772-4030 Fax: ++43 +1 / 42772-4098 email: stefanie.tauber@univie.ac.at www.cibiv.at [[alternative HTML version deleted]]
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You could use the low-level constructor GappedAlignmentPairs(first, last, isProperPair, names=NULL) 'isProperPair' is a logical vector the same length as 'first' and 'last'. For example, GappedAlignmentPairs(left, right, !logical(length(left))) Valerie On 02/27/13 07:12, Stefanie Tauber wrote: > Hi Valerie, > > thanks for the quick answer. > I have already checked how the strand is assigned for paired-end data. > After setting the strand for the left and right parts, > can I somehow rebuild the gappedalignmentPairs object? > > best, > Stefanie > > Am 27.02.2013 um 16:06 schrieb Valerie Obenchain <vobencha at="" fhcrc.org=""> <mailto:vobencha at="" fhcrc.org="">>: > >> Hi Stephanie, >> >> A GappedAlignmentPairs object is made up of a 'left' and a 'right' >> GappedAlignments. >> >> > ex1_file <- system.file("extdata", "ex1.bam", package="Rsamtools") >> > galp <- readGappedAlignmentPairs(ex1_file, use.names=TRUE) >> >> You can extract the left/right parts with an accessor then look at >> strand, cigars, gaps etc. >> >> > left <- left(galp) >> > class(left) >> [1] "GappedAlignments" >> attr(,"package") >> [1] "GenomicRanges" >> >> > strand(left) >> factor-Rle of length 1572 with 665 runs >> Lengths: 3 25 1 1 1 3 1 1 3 2 2 ... 1 6 1 2 3 2 1 5 >> 1 51 >> Values : - + - + - + - + - + - ... + - + - + - + - >> + - >> Levels(3): + - * >> >> > head(cigar(left)) >> [1] "35M" "36M" "35M" "36M" "35M" "35M" >> >> > head(ngap(left)) >> [1] 0 0 0 0 0 0 >> >> It's on these left/right pairs that you can reset the strand. >> >> > strand(left)[1:3] >> factor-Rle of length 3 with 1 run >> Lengths: 3 >> Values : + >> Levels(3): + - * >> > strand(left)[1:3] <- "-" >> > strand(left)[1:3] >> factor-Rle of length 3 with 1 run >> Lengths: 3 >> Values : - >> Levels(3): + - * >> >> Please be sure to read the details on the man page regarding how the >> strands were assigned. >> >> ?GappedAlignmentPairs >> >> >> Valerie >> >> On 02/27/13 05:55, Stefanie Tauber wrote: >>> Dear list, >>> >>> Let's say I have single-end strand-specific RNA-Seq data. >>> Then I could read in the data with: >>> >>> library(GenomicRanges) >>> >>>> reads = readGappedAlignments("data.bam") >>> As I typically don't know which strand has been sequenced, it might >>> be necessary to flip the strand of the reads before doing any kind >>> of summarizeOverlap: >>> >>>> strand(reads) = ifelse(strand(reads) == "+", "-", "+") >>> Now I could do a 'summarizeOverlaps' between the reads and any kind >>> of transcript database. >>> >>> Now, if I have paired-end strand-specific RNA-Seq data. >>> I read the data: >>>> reads = readGappedAlignmentPairs("data.bam") >>> How can I flip the strand of the reads? As it's now paired-end data, >>> it does not work as above. >>> I could imagine several work-arounds, I just wonder if there is any >>> straight approach which I miss at the moment.. >>> >>> >>> best regards, >>> Stefanie >>> >>> >>> >>> >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > DI Stefanie Tauber > > Center for Integrative Bioinformatics Vienna (CIBIV) > (CIBIV is a joint institute of Vienna University and Medical University) > Max F. Perutz Laboratories (MFPL) > Campus Vienna Biocenter 5 (VBC5), Ebene 1, Room 1812.2 > Dr. Bohr Gasse 9 > A-1030 Wien, Austria > Phone: ++43 +1 / 42772-4030 > Fax: ++43 +1 / 42772-4098 > email: stefanie.tauber at univie.ac.at <mailto:stefanie.tauber at="" univie.ac.at=""> > www.cibiv.at <http: www.cibiv.at=""> >
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Hi Stefanie, Val, Makes sense to have a strand setter for GappedAlignmentPairs objects, like we have for GappedAlignments objects. I've added it to GenomicRanges devel: > galp GappedAlignmentPairs with 5 alignment pairs and 0 metadata columns: seqnames strand : ranges -- ranges <rle> <rle> : <iranges> -- <iranges> EAS54_65:6:277:590:364 chr1 - : [ 681, 715] -- [ 503, 537] EAS139_11:5:61:38:1182 chr1 - : [1388, 1422] -- [1205, 1239] EAS188_7:4:21:443:404 chr1 + : [1345, 1379] -- [1529, 1563] EAS1_105:6:23:885:274 chr2 + : [1089, 1123] -- [1289, 1323] EAS1_108:1:65:787:74 chr1 - : [ 213, 247] -- [ 61, 95] --- seqlengths: chr1 chr2 1575 1584 > strand(first(galp)) factor-Rle of length 5 with 3 runs Lengths: 2 2 1 Values : - + - Levels(3): + - * > strand(last(galp)) factor-Rle of length 5 with 3 runs Lengths: 2 2 1 Values : + - + Levels(3): + - * Flip the strand: > strand(galp) <- ifelse(strand(galp) == "+", "-", "+") > galp GappedAlignmentPairs with 5 alignment pairs and 0 metadata columns: seqnames strand : ranges -- ranges <rle> <rle> : <iranges> -- <iranges> EAS54_65:6:277:590:364 chr1 + : [ 681, 715] -- [ 503, 537] EAS139_11:5:61:38:1182 chr1 + : [1388, 1422] -- [1205, 1239] EAS188_7:4:21:443:404 chr1 - : [1345, 1379] -- [1529, 1563] EAS1_105:6:23:885:274 chr2 - : [1089, 1123] -- [1289, 1323] EAS1_108:1:65:787:74 chr1 + : [ 213, 247] -- [ 61, 95] --- seqlengths: chr1 chr2 1575 1584 > strand(first(galp)) factor-Rle of length 5 with 3 runs Lengths: 2 2 1 Values : + - + Levels(3): + - * > strand(last(galp)) factor-Rle of length 5 with 3 runs Lengths: 2 2 1 Values : - + - Levels(3): + - * Note that a slightly more efficient way to compute the flipped strand is: runValue(strand(galp)) <- ifelse(runValue(strand(galp)) == "+", "-", "+") This will only make a difference on big GappedAlignmentPairs objects of course. > sessionInfo() R Under development (unstable) (2013-02-19 r62008) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] Rsamtools_1.11.18 Biostrings_2.27.11 GenomicRanges_1.11.33 [4] IRanges_1.17.35 BiocGenerics_0.5.6 loaded via a namespace (and not attached): [1] bitops_1.0-5 stats4_3.0.0 tools_3.0.0 zlibbioc_1.5.0 GenomicRanges 1.11.33, will become available via biocLite(0 in the next 24 hours or so. Cheers, H. On 02/27/2013 07:48 AM, Valerie Obenchain wrote: > You could use the low-level constructor > > GappedAlignmentPairs(first, last, isProperPair, names=NULL) > > 'isProperPair' is a logical vector the same length as 'first' and > 'last'. For example, > > GappedAlignmentPairs(left, right, !logical(length(left))) > > > Valerie > > On 02/27/13 07:12, Stefanie Tauber wrote: >> Hi Valerie, >> >> thanks for the quick answer. >> I have already checked how the strand is assigned for paired-end data. >> After setting the strand for the left and right parts, >> can I somehow rebuild the gappedalignmentPairs object? >> >> best, >> Stefanie >> >> Am 27.02.2013 um 16:06 schrieb Valerie Obenchain <vobencha at="" fhcrc.org="">> <mailto:vobencha at="" fhcrc.org="">>: >> >>> Hi Stephanie, >>> >>> A GappedAlignmentPairs object is made up of a 'left' and a 'right' >>> GappedAlignments. >>> >>> > ex1_file <- system.file("extdata", "ex1.bam", package="Rsamtools") >>> > galp <- readGappedAlignmentPairs(ex1_file, use.names=TRUE) >>> >>> You can extract the left/right parts with an accessor then look at >>> strand, cigars, gaps etc. >>> >>> > left <- left(galp) >>> > class(left) >>> [1] "GappedAlignments" >>> attr(,"package") >>> [1] "GenomicRanges" >>> >>> > strand(left) >>> factor-Rle of length 1572 with 665 runs >>> Lengths: 3 25 1 1 1 3 1 1 3 2 2 ... 1 6 1 2 3 2 1 5 >>> 1 51 >>> Values : - + - + - + - + - + - ... + - + - + - + - >>> + - >>> Levels(3): + - * >>> >>> > head(cigar(left)) >>> [1] "35M" "36M" "35M" "36M" "35M" "35M" >>> >>> > head(ngap(left)) >>> [1] 0 0 0 0 0 0 >>> >>> It's on these left/right pairs that you can reset the strand. >>> >>> > strand(left)[1:3] >>> factor-Rle of length 3 with 1 run >>> Lengths: 3 >>> Values : + >>> Levels(3): + - * >>> > strand(left)[1:3] <- "-" >>> > strand(left)[1:3] >>> factor-Rle of length 3 with 1 run >>> Lengths: 3 >>> Values : - >>> Levels(3): + - * >>> >>> Please be sure to read the details on the man page regarding how the >>> strands were assigned. >>> >>> ?GappedAlignmentPairs >>> >>> >>> Valerie >>> >>> On 02/27/13 05:55, Stefanie Tauber wrote: >>>> Dear list, >>>> >>>> Let's say I have single-end strand-specific RNA-Seq data. >>>> Then I could read in the data with: >>>> >>>> library(GenomicRanges) >>>> >>>>> reads = readGappedAlignments("data.bam") >>>> As I typically don't know which strand has been sequenced, it might >>>> be necessary to flip the strand of the reads before doing any kind >>>> of summarizeOverlap: >>>> >>>>> strand(reads) = ifelse(strand(reads) == "+", "-", "+") >>>> Now I could do a 'summarizeOverlaps' between the reads and any kind >>>> of transcript database. >>>> >>>> Now, if I have paired-end strand-specific RNA-Seq data. >>>> I read the data: >>>>> reads = readGappedAlignmentPairs("data.bam") >>>> How can I flip the strand of the reads? As it's now paired-end data, >>>> it does not work as above. >>>> I could imagine several work-arounds, I just wonder if there is any >>>> straight approach which I miss at the moment.. >>>> >>>> >>>> best regards, >>>> Stefanie >>>> >>>> >>>> >>>> >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> DI Stefanie Tauber >> >> Center for Integrative Bioinformatics Vienna (CIBIV) >> (CIBIV is a joint institute of Vienna University and Medical University) >> Max F. Perutz Laboratories (MFPL) >> Campus Vienna Biocenter 5 (VBC5), Ebene 1, Room 1812.2 >> Dr. Bohr Gasse 9 >> A-1030 Wien, Austria >> Phone: ++43 +1 / 42772-4030 >> Fax: ++43 +1 / 42772-4098 >> email: stefanie.tauber at univie.ac.at <mailto:stefanie.tauber at="" univie.ac.at=""> >> www.cibiv.at <http: www.cibiv.at=""> >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319
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Thanks Herve. On 02/27/13 11:23, Hervé Pagès wrote: > Hi Stefanie, Val, > > Makes sense to have a strand setter for GappedAlignmentPairs > objects, like we have for GappedAlignments objects. I've added > it to GenomicRanges devel: > > > galp > GappedAlignmentPairs with 5 alignment pairs and 0 metadata columns: > seqnames strand : ranges -- ranges > <rle> <rle> : <iranges> -- <iranges> > EAS54_65:6:277:590:364 chr1 - : [ 681, 715] -- [ 503, 537] > EAS139_11:5:61:38:1182 chr1 - : [1388, 1422] -- [1205, 1239] > EAS188_7:4:21:443:404 chr1 + : [1345, 1379] -- [1529, 1563] > EAS1_105:6:23:885:274 chr2 + : [1089, 1123] -- [1289, 1323] > EAS1_108:1:65:787:74 chr1 - : [ 213, 247] -- [ 61, 95] > --- > seqlengths: > chr1 chr2 > 1575 1584 > > > strand(first(galp)) > factor-Rle of length 5 with 3 runs > Lengths: 2 2 1 > Values : - + - > Levels(3): + - * > > > strand(last(galp)) > factor-Rle of length 5 with 3 runs > Lengths: 2 2 1 > Values : + - + > Levels(3): + - * > > Flip the strand: > > > strand(galp) <- ifelse(strand(galp) == "+", "-", "+") > > galp > GappedAlignmentPairs with 5 alignment pairs and 0 metadata columns: > seqnames strand : ranges -- ranges > <rle> <rle> : <iranges> -- <iranges> > EAS54_65:6:277:590:364 chr1 + : [ 681, 715] -- [ 503, 537] > EAS139_11:5:61:38:1182 chr1 + : [1388, 1422] -- [1205, 1239] > EAS188_7:4:21:443:404 chr1 - : [1345, 1379] -- [1529, 1563] > EAS1_105:6:23:885:274 chr2 - : [1089, 1123] -- [1289, 1323] > EAS1_108:1:65:787:74 chr1 + : [ 213, 247] -- [ 61, 95] > --- > seqlengths: > chr1 chr2 > 1575 1584 > > > strand(first(galp)) > factor-Rle of length 5 with 3 runs > Lengths: 2 2 1 > Values : + - + > Levels(3): + - * > > > strand(last(galp)) > factor-Rle of length 5 with 3 runs > Lengths: 2 2 1 > Values : - + - > Levels(3): + - * > > Note that a slightly more efficient way to compute the flipped strand > is: > > runValue(strand(galp)) <- ifelse(runValue(strand(galp)) == "+", > "-", "+") > > This will only make a difference on big GappedAlignmentPairs objects of > course. > > > sessionInfo() > R Under development (unstable) (2013-02-19 r62008) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] Rsamtools_1.11.18 Biostrings_2.27.11 GenomicRanges_1.11.33 > [4] IRanges_1.17.35 BiocGenerics_0.5.6 > > loaded via a namespace (and not attached): > [1] bitops_1.0-5 stats4_3.0.0 tools_3.0.0 zlibbioc_1.5.0 > > > GenomicRanges 1.11.33, will become available via biocLite(0 in the next > 24 hours or so. > > Cheers, > H. > > > On 02/27/2013 07:48 AM, Valerie Obenchain wrote: >> You could use the low-level constructor >> >> GappedAlignmentPairs(first, last, isProperPair, names=NULL) >> >> 'isProperPair' is a logical vector the same length as 'first' and >> 'last'. For example, >> >> GappedAlignmentPairs(left, right, !logical(length(left))) >> >> >> Valerie >> >> On 02/27/13 07:12, Stefanie Tauber wrote: >>> Hi Valerie, >>> >>> thanks for the quick answer. >>> I have already checked how the strand is assigned for paired-end data. >>> After setting the strand for the left and right parts, >>> can I somehow rebuild the gappedalignmentPairs object? >>> >>> best, >>> Stefanie >>> >>> Am 27.02.2013 um 16:06 schrieb Valerie Obenchain <vobencha at="" fhcrc.org="">>> <mailto:vobencha at="" fhcrc.org="">>: >>> >>>> Hi Stephanie, >>>> >>>> A GappedAlignmentPairs object is made up of a 'left' and a 'right' >>>> GappedAlignments. >>>> >>>> > ex1_file <- system.file("extdata", "ex1.bam", package="Rsamtools") >>>> > galp <- readGappedAlignmentPairs(ex1_file, use.names=TRUE) >>>> >>>> You can extract the left/right parts with an accessor then look at >>>> strand, cigars, gaps etc. >>>> >>>> > left <- left(galp) >>>> > class(left) >>>> [1] "GappedAlignments" >>>> attr(,"package") >>>> [1] "GenomicRanges" >>>> >>>> > strand(left) >>>> factor-Rle of length 1572 with 665 runs >>>> Lengths: 3 25 1 1 1 3 1 1 3 2 2 ... 1 6 1 2 3 2 1 5 >>>> 1 51 >>>> Values : - + - + - + - + - + - ... + - + - + - + - >>>> + - >>>> Levels(3): + - * >>>> >>>> > head(cigar(left)) >>>> [1] "35M" "36M" "35M" "36M" "35M" "35M" >>>> >>>> > head(ngap(left)) >>>> [1] 0 0 0 0 0 0 >>>> >>>> It's on these left/right pairs that you can reset the strand. >>>> >>>> > strand(left)[1:3] >>>> factor-Rle of length 3 with 1 run >>>> Lengths: 3 >>>> Values : + >>>> Levels(3): + - * >>>> > strand(left)[1:3] <- "-" >>>> > strand(left)[1:3] >>>> factor-Rle of length 3 with 1 run >>>> Lengths: 3 >>>> Values : - >>>> Levels(3): + - * >>>> >>>> Please be sure to read the details on the man page regarding how the >>>> strands were assigned. >>>> >>>> ?GappedAlignmentPairs >>>> >>>> >>>> Valerie >>>> >>>> On 02/27/13 05:55, Stefanie Tauber wrote: >>>>> Dear list, >>>>> >>>>> Let's say I have single-end strand-specific RNA-Seq data. >>>>> Then I could read in the data with: >>>>> >>>>> library(GenomicRanges) >>>>> >>>>>> reads = readGappedAlignments("data.bam") >>>>> As I typically don't know which strand has been sequenced, it might >>>>> be necessary to flip the strand of the reads before doing any kind >>>>> of summarizeOverlap: >>>>> >>>>>> strand(reads) = ifelse(strand(reads) == "+", "-", "+") >>>>> Now I could do a 'summarizeOverlaps' between the reads and any kind >>>>> of transcript database. >>>>> >>>>> Now, if I have paired-end strand-specific RNA-Seq data. >>>>> I read the data: >>>>>> reads = readGappedAlignmentPairs("data.bam") >>>>> How can I flip the strand of the reads? As it's now paired-end data, >>>>> it does not work as above. >>>>> I could imagine several work-arounds, I just wonder if there is any >>>>> straight approach which I miss at the moment.. >>>>> >>>>> >>>>> best regards, >>>>> Stefanie >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> [[alternative HTML version deleted]] >>>>> >>>>> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: >>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>> >>> DI Stefanie Tauber >>> >>> Center for Integrative Bioinformatics Vienna (CIBIV) >>> (CIBIV is a joint institute of Vienna University and Medical >>> University) >>> Max F. Perutz Laboratories (MFPL) >>> Campus Vienna Biocenter 5 (VBC5), Ebene 1, Room 1812.2 >>> Dr. Bohr Gasse 9 >>> A-1030 Wien, Austria >>> Phone: ++43 +1 / 42772-4030 >>> Fax: ++43 +1 / 42772-4098 >>> email: stefanie.tauber at univie.ac.at >>> <mailto:stefanie.tauber at="" univie.ac.at=""> >>> www.cibiv.at <http: www.cibiv.at=""> >>> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >
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Thanks a lot to both of you! Best, Stefanie Am 27.02.2013 um 20:47 schrieb Valerie Obenchain <vobencha at="" fhcrc.org="">: > Thanks Herve. > > On 02/27/13 11:23, Hervé Pagès wrote: >> Hi Stefanie, Val, >> >> Makes sense to have a strand setter for GappedAlignmentPairs >> objects, like we have for GappedAlignments objects. I've added >> it to GenomicRanges devel: >> >> > galp >> GappedAlignmentPairs with 5 alignment pairs and 0 metadata columns: >> seqnames strand : ranges -- ranges >> <rle> <rle> : <iranges> -- <iranges> >> EAS54_65:6:277:590:364 chr1 - : [ 681, 715] -- [ 503, 537] >> EAS139_11:5:61:38:1182 chr1 - : [1388, 1422] -- [1205, 1239] >> EAS188_7:4:21:443:404 chr1 + : [1345, 1379] -- [1529, 1563] >> EAS1_105:6:23:885:274 chr2 + : [1089, 1123] -- [1289, 1323] >> EAS1_108:1:65:787:74 chr1 - : [ 213, 247] -- [ 61, 95] >> --- >> seqlengths: >> chr1 chr2 >> 1575 1584 >> >> > strand(first(galp)) >> factor-Rle of length 5 with 3 runs >> Lengths: 2 2 1 >> Values : - + - >> Levels(3): + - * >> >> > strand(last(galp)) >> factor-Rle of length 5 with 3 runs >> Lengths: 2 2 1 >> Values : + - + >> Levels(3): + - * >> >> Flip the strand: >> >> > strand(galp) <- ifelse(strand(galp) == "+", "-", "+") >> > galp >> GappedAlignmentPairs with 5 alignment pairs and 0 metadata columns: >> seqnames strand : ranges -- ranges >> <rle> <rle> : <iranges> -- <iranges> >> EAS54_65:6:277:590:364 chr1 + : [ 681, 715] -- [ 503, 537] >> EAS139_11:5:61:38:1182 chr1 + : [1388, 1422] -- [1205, 1239] >> EAS188_7:4:21:443:404 chr1 - : [1345, 1379] -- [1529, 1563] >> EAS1_105:6:23:885:274 chr2 - : [1089, 1123] -- [1289, 1323] >> EAS1_108:1:65:787:74 chr1 + : [ 213, 247] -- [ 61, 95] >> --- >> seqlengths: >> chr1 chr2 >> 1575 1584 >> >> > strand(first(galp)) >> factor-Rle of length 5 with 3 runs >> Lengths: 2 2 1 >> Values : + - + >> Levels(3): + - * >> >> > strand(last(galp)) >> factor-Rle of length 5 with 3 runs >> Lengths: 2 2 1 >> Values : - + - >> Levels(3): + - * >> >> Note that a slightly more efficient way to compute the flipped strand >> is: >> >> runValue(strand(galp)) <- ifelse(runValue(strand(galp)) == "+", >> "-", "+") >> >> This will only make a difference on big GappedAlignmentPairs objects of >> course. >> >> > sessionInfo() >> R Under development (unstable) (2013-02-19 r62008) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=C LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets methods >> [8] base >> >> other attached packages: >> [1] Rsamtools_1.11.18 Biostrings_2.27.11 GenomicRanges_1.11.33 >> [4] IRanges_1.17.35 BiocGenerics_0.5.6 >> >> loaded via a namespace (and not attached): >> [1] bitops_1.0-5 stats4_3.0.0 tools_3.0.0 zlibbioc_1.5.0 >> >> >> GenomicRanges 1.11.33, will become available via biocLite(0 in the next >> 24 hours or so. >> >> Cheers, >> H. >> >> >> On 02/27/2013 07:48 AM, Valerie Obenchain wrote: >>> You could use the low-level constructor >>> >>> GappedAlignmentPairs(first, last, isProperPair, names=NULL) >>> >>> 'isProperPair' is a logical vector the same length as 'first' and >>> 'last'. For example, >>> >>> GappedAlignmentPairs(left, right, !logical(length(left))) >>> >>> >>> Valerie >>> >>> On 02/27/13 07:12, Stefanie Tauber wrote: >>>> Hi Valerie, >>>> >>>> thanks for the quick answer. >>>> I have already checked how the strand is assigned for paired-end data. >>>> After setting the strand for the left and right parts, >>>> can I somehow rebuild the gappedalignmentPairs object? >>>> >>>> best, >>>> Stefanie >>>> >>>> Am 27.02.2013 um 16:06 schrieb Valerie Obenchain <vobencha at="" fhcrc.org="">>>> <mailto:vobencha at="" fhcrc.org="">>: >>>> >>>>> Hi Stephanie, >>>>> >>>>> A GappedAlignmentPairs object is made up of a 'left' and a 'right' >>>>> GappedAlignments. >>>>> >>>>> > ex1_file <- system.file("extdata", "ex1.bam", package="Rsamtools") >>>>> > galp <- readGappedAlignmentPairs(ex1_file, use.names=TRUE) >>>>> >>>>> You can extract the left/right parts with an accessor then look at >>>>> strand, cigars, gaps etc. >>>>> >>>>> > left <- left(galp) >>>>> > class(left) >>>>> [1] "GappedAlignments" >>>>> attr(,"package") >>>>> [1] "GenomicRanges" >>>>> >>>>> > strand(left) >>>>> factor-Rle of length 1572 with 665 runs >>>>> Lengths: 3 25 1 1 1 3 1 1 3 2 2 ... 1 6 1 2 3 2 1 5 >>>>> 1 51 >>>>> Values : - + - + - + - + - + - ... + - + - + - + - >>>>> + - >>>>> Levels(3): + - * >>>>> >>>>> > head(cigar(left)) >>>>> [1] "35M" "36M" "35M" "36M" "35M" "35M" >>>>> >>>>> > head(ngap(left)) >>>>> [1] 0 0 0 0 0 0 >>>>> >>>>> It's on these left/right pairs that you can reset the strand. >>>>> >>>>> > strand(left)[1:3] >>>>> factor-Rle of length 3 with 1 run >>>>> Lengths: 3 >>>>> Values : + >>>>> Levels(3): + - * >>>>> > strand(left)[1:3] <- "-" >>>>> > strand(left)[1:3] >>>>> factor-Rle of length 3 with 1 run >>>>> Lengths: 3 >>>>> Values : - >>>>> Levels(3): + - * >>>>> >>>>> Please be sure to read the details on the man page regarding how the >>>>> strands were assigned. >>>>> >>>>> ?GappedAlignmentPairs >>>>> >>>>> >>>>> Valerie >>>>> >>>>> On 02/27/13 05:55, Stefanie Tauber wrote: >>>>>> Dear list, >>>>>> >>>>>> Let's say I have single-end strand-specific RNA-Seq data. >>>>>> Then I could read in the data with: >>>>>> >>>>>> library(GenomicRanges) >>>>>> >>>>>>> reads = readGappedAlignments("data.bam") >>>>>> As I typically don't know which strand has been sequenced, it might >>>>>> be necessary to flip the strand of the reads before doing any kind >>>>>> of summarizeOverlap: >>>>>> >>>>>>> strand(reads) = ifelse(strand(reads) == "+", "-", "+") >>>>>> Now I could do a 'summarizeOverlaps' between the reads and any kind >>>>>> of transcript database. >>>>>> >>>>>> Now, if I have paired-end strand-specific RNA-Seq data. >>>>>> I read the data: >>>>>>> reads = readGappedAlignmentPairs("data.bam") >>>>>> How can I flip the strand of the reads? As it's now paired-end data, >>>>>> it does not work as above. >>>>>> I could imagine several work-arounds, I just wonder if there is any >>>>>> straight approach which I miss at the moment.. >>>>>> >>>>>> >>>>>> best regards, >>>>>> Stefanie >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> [[alternative HTML version deleted]] >>>>>> >>>>>> _______________________________________________ >>>>>> Bioconductor mailing list >>>>>> Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> >>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>> Search the archives: >>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>
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