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Question: Calculate coverage on genome.
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gravatar for Fabrice Tourre
6.7 years ago by
Fabrice Tourre950 wrote:
Dear list, I am analysis mouse MeDIP-seq data, I want to know what percent reads coveraged the promter, 3'UTR, 5'UTR, intron and Exon region. Is there any packages can do this? Thank you very much in advance.
ADD COMMENTlink modified 6.7 years ago • written 6.7 years ago by Fabrice Tourre950
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gravatar for Fabrice Tourre
6.7 years ago by
Fabrice Tourre950 wrote:
What's more, how many covaged the repeat region and unique region? On Tue, Mar 15, 2011 at 8:18 PM, Fabrice Tourre <fabrice.ciup at="" gmail.com=""> wrote: > Dear list, > I am analysis mouse MeDIP-seq data, I want to know what percent reads > coveraged the promter, 3'UTR, 5'UTR, intron and Exon region. Is there > any packages can do this? > Thank you very much in advance. >
ADD COMMENTlink written 6.7 years ago by Fabrice Tourre950
On 03/15/2011 12:19 PM, Fabrice Tourre wrote: > What's more, how many covaged the repeat region and unique region? Hi Fabrice -- The steps in the work flow might invovle: input reads library(GenomicRanges) aln <- readGappedAlignemnts(<...>)) and create regions of interest, e.g., from library(GenomicFeatures) txdb <- makeTranscriptDbFromUCSC(<...>) cds <- cdsBy(txdb, "gene") or using the biomaRt or AnnotationDbi packages. Then count reads in each region of interest hits <- countOverlaps(aln, cds) or calculate coverage and take views based on your regions of interest cvg <- coverage(aln) v <- Views(cvg, ranges(cds)) and then summarize, e.g., viewSums. Maybe others will contribute more detail. Martin > > On Tue, Mar 15, 2011 at 8:18 PM, Fabrice Tourre<fabrice.ciup at="" gmail.com=""> wrote: >> Dear list, >> I am analysis mouse MeDIP-seq data, I want to know what percent reads >> coveraged the promter, 3'UTR, 5'UTR, intron and Exon region. Is there >> any packages can do this? >> Thank you very much in advance. >> > > _______________________________________________ > 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 -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
ADD REPLYlink written 6.7 years ago by Martin Morgan ♦♦ 20k
Dear Martin, I am appreciated for you suggestion. I found in GenomicFeatures, there are such method: transcriptsBy, exonsBy, cdsBy, intronsByTranscript, fiveUTRsByTranscript, threeUTRsByTranscript. So maybe I can used these method to got the coverage on exons, cds, transcripts, introns, 3'utr and 5'utr. Do you have some ideas how to got the coverages on promoter regions? For example, up to TSS 5kb regions. Thanks. On Tue, Mar 15, 2011 at 9:17 PM, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: > On 03/15/2011 12:19 PM, Fabrice Tourre wrote: >> >> What's more, how many covaged the repeat region and unique region? > > Hi Fabrice -- > > The steps in the work flow might invovle: input reads > > ?library(GenomicRanges) > ?aln <- readGappedAlignemnts(<...>)) > > and create regions of interest, e.g., from > > ?library(GenomicFeatures) > ?txdb <- makeTranscriptDbFromUCSC(<...>) > ?cds <- cdsBy(txdb, "gene") > > or using the biomaRt or AnnotationDbi packages. Then count reads in each > region of interest > > ?hits <- countOverlaps(aln, cds) > > or calculate coverage and take views based on your regions of interest > > ?cvg <- coverage(aln) > ?v <- Views(cvg, ranges(cds)) > > and then summarize, e.g., viewSums. Maybe others will contribute more > detail. > > Martin > >> >> On Tue, Mar 15, 2011 at 8:18 PM, Fabrice Tourre<fabrice.ciup at="" gmail.com=""> >> ?wrote: >>> >>> Dear list, >>> I am analysis mouse MeDIP-seq data, I want to know what percent reads >>> coveraged the promter, 3'UTR, 5'UTR, intron and Exon region. Is there >>> any packages can do this? >>> Thank you very much in advance. >>> >> >> _______________________________________________ >> 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 > > > -- > Computational Biology > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 > > Location: M1-B861 > Telephone: 206 667-2793 > > _______________________________________________ > 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 >
ADD REPLYlink written 6.7 years ago by Fabrice Tourre950
On 03/16/2011 01:46 AM, Fabrice Tourre wrote: > Dear Martin, > I am appreciated for you suggestion. > I found in GenomicFeatures, there are such method: > transcriptsBy, exonsBy, cdsBy, intronsByTranscript, > fiveUTRsByTranscript, threeUTRsByTranscript. > > So maybe I can used these method to got the coverage on exons, cds, > transcripts, introns, 3'utr and 5'utr. Do you have some ideas how to > got the coverages on promoter regions? For example, up to TSS 5kb > regions. Hi Fabrice -- if you have the TSS (e.g., from start(transcriptsBy(<...))), you can easily create GRanges representing them, either directly using ?GRanges or ?GRangesList, or by manipulating an existing GRanges / GRangesList object with commands like flank, narrow, etc., as documented on for instance the GRanes help page. Martin > Thanks. > > On Tue, Mar 15, 2011 at 9:17 PM, Martin Morgan<mtmorgan at="" fhcrc.org=""> wrote: >> On 03/15/2011 12:19 PM, Fabrice Tourre wrote: >>> >>> What's more, how many covaged the repeat region and unique region? >> >> Hi Fabrice -- >> >> The steps in the work flow might invovle: input reads >> >> library(GenomicRanges) >> aln<- readGappedAlignemnts(<...>)) >> >> and create regions of interest, e.g., from >> >> library(GenomicFeatures) >> txdb<- makeTranscriptDbFromUCSC(<...>) >> cds<- cdsBy(txdb, "gene") >> >> or using the biomaRt or AnnotationDbi packages. Then count reads in each >> region of interest >> >> hits<- countOverlaps(aln, cds) >> >> or calculate coverage and take views based on your regions of interest >> >> cvg<- coverage(aln) >> v<- Views(cvg, ranges(cds)) >> >> and then summarize, e.g., viewSums. Maybe others will contribute more >> detail. >> >> Martin >> >>> >>> On Tue, Mar 15, 2011 at 8:18 PM, Fabrice Tourre<fabrice.ciup at="" gmail.com=""> >>> wrote: >>>> >>>> Dear list, >>>> I am analysis mouse MeDIP-seq data, I want to know what percent reads >>>> coveraged the promter, 3'UTR, 5'UTR, intron and Exon region. Is there >>>> any packages can do this? >>>> Thank you very much in advance. >>>> >>> >>> _______________________________________________ >>> 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 >> >> >> -- >> Computational Biology >> Fred Hutchinson Cancer Research Center >> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 >> >> Location: M1-B861 >> Telephone: 206 667-2793 >> >> _______________________________________________ >> 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 >> -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
ADD REPLYlink written 6.7 years ago by Martin Morgan ♦♦ 20k
Dear Martin, Thank you very much for your help. It seems I have got it with your help. In fact, I have read the manual of IRanges a few days ago. But it is difficult to understand what is doing of methods flank, narrow, restrict, etc. I think the best written documents are bedtools. Just a complain. I will have a closer look again. Thanks. On Wed, Mar 16, 2011 at 2:25 PM, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: > On 03/16/2011 01:46 AM, Fabrice Tourre wrote: >> >> Dear Martin, >> I am appreciated for you suggestion. >> I found in GenomicFeatures, there are such method: >> transcriptsBy, exonsBy, cdsBy, intronsByTranscript, >> fiveUTRsByTranscript, threeUTRsByTranscript. >> >> So maybe I can used these method to got the coverage on exons, cds, >> transcripts, introns, 3'utr and 5'utr. Do you have some ideas how to >> got the coverages on promoter regions? For example, up to TSS 5kb >> regions. > > Hi Fabrice -- if you have the TSS (e.g., from start(transcriptsBy(<...))), > you can easily create GRanges representing them, either directly using > ?GRanges or ?GRangesList, or by manipulating an existing GRanges / > GRangesList object with commands like flank, narrow, etc., as documented on > for instance the GRanes help page. Martin > >> Thanks. >> >> On Tue, Mar 15, 2011 at 9:17 PM, Martin Morgan<mtmorgan at="" fhcrc.org=""> ?wrote: >>> >>> On 03/15/2011 12:19 PM, Fabrice Tourre wrote: >>>> >>>> What's more, how many covaged the repeat region and unique region? >>> >>> Hi Fabrice -- >>> >>> The steps in the work flow might invovle: input reads >>> >>> ?library(GenomicRanges) >>> ?aln<- readGappedAlignemnts(<...>)) >>> >>> and create regions of interest, e.g., from >>> >>> ?library(GenomicFeatures) >>> ?txdb<- makeTranscriptDbFromUCSC(<...>) >>> ?cds<- cdsBy(txdb, "gene") >>> >>> or using the biomaRt or AnnotationDbi packages. Then count reads in each >>> region of interest >>> >>> ?hits<- countOverlaps(aln, cds) >>> >>> or calculate coverage and take views based on your regions of interest >>> >>> ?cvg<- coverage(aln) >>> ?v<- Views(cvg, ranges(cds)) >>> >>> and then summarize, e.g., viewSums. Maybe others will contribute more >>> detail. >>> >>> Martin >>> >>>> >>>> On Tue, Mar 15, 2011 at 8:18 PM, Fabrice Tourre<fabrice.ciup at="" gmail.com=""> >>>> ?wrote: >>>>> >>>>> Dear list, >>>>> I am analysis mouse MeDIP-seq data, I want to know what percent reads >>>>> coveraged the promter, 3'UTR, 5'UTR, intron and Exon region. Is there >>>>> any packages can do this? >>>>> Thank you very much in advance. >>>>> >>>> >>>> _______________________________________________ >>>> 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 >>> >>> >>> -- >>> Computational Biology >>> Fred Hutchinson Cancer Research Center >>> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 >>> >>> Location: M1-B861 >>> Telephone: 206 667-2793 >>> >>> _______________________________________________ >>> 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 >>> > > > -- > Computational Biology > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 > > Location: M1-B861 > Telephone: 206 667-2793 > > _______________________________________________ > 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 >
ADD REPLYlink written 6.7 years ago by Fabrice Tourre950
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