Where is DEXSeq bioconductor package?
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Jinyan Huang ▴ 190
@jinyan-huang-4157
Last seen 8.4 years ago
When I download and install, I got this error. R CMD INSTALL DEXSeq_0.1.12.tar.gz * installing to library '~/R/x86_64-pc-linux-gnu-library/2.12' ERROR: dependency 'stringr' is not available for package 'DEXSeq' * removing '~/R/x86_64-pc-linux-gnu-library/2.12/DEXSeq' sessionInfo() R version 2.12.1 (2010-12-16) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.12.1 On Mon, Jul 25, 2011 at 4:17 PM, Simon Anders <anders at="" embl.de=""> wrote: > Hi > > Just to clarify: As indicated by the fact that it is available in the devel > branch only and not in release branch, DEXSeq is not yet released, and it > has not yet gone through the official Bioconductor peer review process > required for inclusion in the release. > > DEXSeq is more or less finished even though we are still busy with some > polishing and testing. If you want to try out the current beta version, go > ahead, but please be aware that there might still be a few rough corners. > Any feed-back is most welcome, of course. > > ?Simon > > _______________________________________________ > 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 >
DEXSeq DEXSeq • 1.4k views
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@sean-davis-490
Last seen 5 months ago
United States
Hi. As Simon and I pointed out, you will need to run R-devel to access DEXseq. Also, the install procedure for bioconductor packages is detailed on the website, but it is basically: source("http://bioconductor.org/biocLite.R") biocLite('DEXseq') If after updating R and following the above instructions you still have problems, write back to the list. Sean On Thu, Aug 4, 2011 at 8:26 AM, Jinyan Huang <jhuang.ceph at="" gmail.com=""> wrote: > When I download and install, I got this error. > > R CMD INSTALL ?DEXSeq_0.1.12.tar.gz > * installing to library '~/R/x86_64-pc-linux-gnu-library/2.12' > ERROR: dependency 'stringr' is not available for package 'DEXSeq' > * removing '~/R/x86_64-pc-linux-gnu-library/2.12/DEXSeq' > > sessionInfo() > R version 2.12.1 (2010-12-16) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] C > > attached base packages: > [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base > > loaded via a namespace (and not attached): > [1] tools_2.12.1 > > On Mon, Jul 25, 2011 at 4:17 PM, Simon Anders <anders at="" embl.de=""> wrote: >> Hi >> >> Just to clarify: As indicated by the fact that it is available in the devel >> branch only and not in release branch, DEXSeq is not yet released, and it >> has not yet gone through the official Bioconductor peer review process >> required for inclusion in the release. >> >> DEXSeq is more or less finished even though we are still busy with some >> polishing and testing. If you want to try out the current beta version, go >> ahead, but please be aware that there might still be a few rough corners. >> Any feed-back is most welcome, of course. >> >> ?Simon >> >> _______________________________________________ >> 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 >> > > _______________________________________________ > 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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When I run python script dexseq_count.py in DEXseq. I have these error. ~/bin/python/python /env/ins/home/user/bin/dexseq_count.py -p yes -s yes -a 10 /env/ins/home/user/rna-seq/info/DEX-63.gtf ~/rna-seq/exp/data/mapping/bwa/7005_4.sam test.count /env/ins/home/user/bin/python/lib/python2.7/site- packages/HTSeq-0.5.3p1-py2.7-linux-x86_64.egg/HTSeq/__init__.py:543: UserWarning: Malformed SAM line: MRNM != '*' although flag bit &0x0008 set algnt = SAM_Alignment.from_SAM_line( line ) /env/ins/home/user/bin/python/lib/python2.7/site- packages/HTSeq-0.5.3p1-py2.7-linux-x86_64.egg/HTSeq/__init__.py:543: UserWarning: Malformed SAM line: RNAME != '*' although flag bit &0x0004 set algnt = SAM_Alignment.from_SAM_line( line ) Traceback (most recent call last): File "/env/ins/home/user/bin/rnaseq/pipeline/dexseq_count.py", line 138, in <module> counts[ '_loqaqual' ] += 1 KeyError: '_loqaqual' Python:2.7 HTSeq:0.5.3p1 DEXseq:0.1.12 Sam produced by bwa (bwa-0.5.9) against Ensembl 63 (Human, RNA-seq pair-end sample). It seems that BWA convert all the reads to forward strand, so I set -s yes. Is it right? Thank you.
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On Thu, Aug 4, 2011 at 11:41 AM, Fabrice Tourre <fabrice.ciup at="" gmail.com=""> wrote: > When I run python script dexseq_count.py in DEXseq. I have these error. > > ~/bin/python/python /env/ins/home/user/bin/dexseq_count.py -p yes -s > yes -a 10 /env/ins/home/user/rna-seq/info/DEX-63.gtf > ~/rna-seq/exp/data/mapping/bwa/7005_4.sam test.count > > /env/ins/home/user/bin/python/lib/python2.7/site- packages/HTSeq-0.5.3p1-py2.7-linux-x86_64.egg/HTSeq/__init__.py:543: > UserWarning: Malformed SAM line: MRNM != '*' although flag bit &0x0008 > set > ?algnt = SAM_Alignment.from_SAM_line( line ) > /env/ins/home/user/bin/python/lib/python2.7/site- packages/HTSeq-0.5.3p1-py2.7-linux-x86_64.egg/HTSeq/__init__.py:543: > UserWarning: Malformed SAM line: RNAME != '*' although flag bit > &0x0004 set > ?algnt = SAM_Alignment.from_SAM_line( line ) > Traceback (most recent call last): > ?File "/env/ins/home/user/bin/rnaseq/pipeline/dexseq_count.py", line > 138, in <module> > ? ?counts[ '_loqaqual' ] += 1 > KeyError: '_loqaqual' > > > Python:2.7 > HTSeq:0.5.3p1 > DEXseq:0.1.12 > Sam produced by bwa (bwa-0.5.9) against Ensembl 63 (Human, RNA-seq > pair-end sample). > It seems that BWA convert all the reads to forward strand, so I set -s > yes. Is it right? I do not think that BWA "converts" all reads to the forward strand, although I may be misunderstanding what you mean by "converts". The strand information is encoded in the FLAG column. See here: http://samtools.sourceforge.net/SAM1.pdf Sean
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In bwa, the sequence presented in the sam/bam file is always the sequence in the forward orientation relative to the reference. If it maps to the reverse strand, then bwa reverse complements the read sequence (and reverses the quality string) before writing it to the sam/bam file. Is it right? Thank you. On Thu, Aug 4, 2011 at 5:50 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > On Thu, Aug 4, 2011 at 11:41 AM, Fabrice Tourre <fabrice.ciup at="" gmail.com=""> wrote: >> When I run python script dexseq_count.py in DEXseq. I have these error. >> >> ~/bin/python/python /env/ins/home/user/bin/dexseq_count.py -p yes -s >> yes -a 10 /env/ins/home/user/rna-seq/info/DEX-63.gtf >> ~/rna-seq/exp/data/mapping/bwa/7005_4.sam test.count >> >> /env/ins/home/user/bin/python/lib/python2.7/site- packages/HTSeq-0.5.3p1-py2.7-linux-x86_64.egg/HTSeq/__init__.py:543: >> UserWarning: Malformed SAM line: MRNM != '*' although flag bit &0x0008 >> set >> ?algnt = SAM_Alignment.from_SAM_line( line ) >> /env/ins/home/user/bin/python/lib/python2.7/site- packages/HTSeq-0.5.3p1-py2.7-linux-x86_64.egg/HTSeq/__init__.py:543: >> UserWarning: Malformed SAM line: RNAME != '*' although flag bit >> &0x0004 set >> ?algnt = SAM_Alignment.from_SAM_line( line ) >> Traceback (most recent call last): >> ?File "/env/ins/home/user/bin/rnaseq/pipeline/dexseq_count.py", line >> 138, in <module> >> ? ?counts[ '_loqaqual' ] += 1 >> KeyError: '_loqaqual' >> >> >> Python:2.7 >> HTSeq:0.5.3p1 >> DEXseq:0.1.12 >> Sam produced by bwa (bwa-0.5.9) against Ensembl 63 (Human, RNA-seq >> pair-end sample). >> It seems that BWA convert all the reads to forward strand, so I set -s >> yes. Is it right? > > I do not think that BWA "converts" all reads to the forward strand, > although I may be misunderstanding what you mean by "converts". ?The > strand information is encoded in the FLAG column. ?See here: > > http://samtools.sourceforge.net/SAM1.pdf > > Sean >
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On Thu, Aug 4, 2011 at 12:11 PM, Fabrice Tourre <fabrice.ciup at="" gmail.com=""> wrote: > In bwa, the sequence presented in the sam/bam file is always the > sequence in the forward orientation relative to the reference. If it > maps to the reverse strand, then bwa reverse complements the read > sequence (and reverses the quality string) before writing it to the > sam/bam file. ?Is it right? I believe that is correct, yes, for the sequence itself; this is not specific to BWA as this is how the SAM format works. Sorry for my confusion in your last email. Sean > On Thu, Aug 4, 2011 at 5:50 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: >> On Thu, Aug 4, 2011 at 11:41 AM, Fabrice Tourre <fabrice.ciup at="" gmail.com=""> wrote: >>> When I run python script dexseq_count.py in DEXseq. I have these error. >>> >>> ~/bin/python/python /env/ins/home/user/bin/dexseq_count.py -p yes -s >>> yes -a 10 /env/ins/home/user/rna-seq/info/DEX-63.gtf >>> ~/rna-seq/exp/data/mapping/bwa/7005_4.sam test.count >>> >>> /env/ins/home/user/bin/python/lib/python2.7/site- packages/HTSeq-0.5.3p1-py2.7-linux-x86_64.egg/HTSeq/__init__.py:543: >>> UserWarning: Malformed SAM line: MRNM != '*' although flag bit &0x0008 >>> set >>> ?algnt = SAM_Alignment.from_SAM_line( line ) >>> /env/ins/home/user/bin/python/lib/python2.7/site- packages/HTSeq-0.5.3p1-py2.7-linux-x86_64.egg/HTSeq/__init__.py:543: >>> UserWarning: Malformed SAM line: RNAME != '*' although flag bit >>> &0x0004 set >>> ?algnt = SAM_Alignment.from_SAM_line( line ) >>> Traceback (most recent call last): >>> ?File "/env/ins/home/user/bin/rnaseq/pipeline/dexseq_count.py", line >>> 138, in <module> >>> ? ?counts[ '_loqaqual' ] += 1 >>> KeyError: '_loqaqual' >>> >>> >>> Python:2.7 >>> HTSeq:0.5.3p1 >>> DEXseq:0.1.12 >>> Sam produced by bwa (bwa-0.5.9) against Ensembl 63 (Human, RNA-seq >>> pair-end sample). >>> It seems that BWA convert all the reads to forward strand, so I set -s >>> yes. Is it right? >> >> I do not think that BWA "converts" all reads to the forward strand, >> although I may be misunderstanding what you mean by "converts". ?The >> strand information is encoded in the FLAG column. ?See here: >> >> http://samtools.sourceforge.net/SAM1.pdf >> >> Sean >> > > _______________________________________________ > 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 On 08/04/2011 06:11 PM, Fabrice Tourre wrote: >>> It seems that BWA convert all the reads to forward strand, so I set -s >>> yes. Is it right? The SAM format specifies that for reads mapped to the reverse strand, not the sequenced read but its reverse complement is stored. However, the '-s' switch has nothing to do with this. It is about whether you data is strand-specific, i.e., whether the strand to which a read has been aligned is the template strand of the actual transcript. (In standard RNA-Seq, the strand information is lost; newer protocols preserve it by ligating adapters before rather than after second- strand synthesis. The counting script needs to know which type of protocol you have used.) S
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Simon, Thanks. I am curios what is the potential problem we will have if the -s parameters set wrong? If there is a way to know the -s parameters from the data? When I run dexseq_count.py on my sam file from bwa, it always has this warning: ~/python/lib/python2.7/site-packages/HTSeq-0.5.3p1-py2.7-linux- x86_64.egg/HTSeq/__init__.py:543: UserWarning: Malformed SAM line: RNAME != '*' although flag bit &0x0004 set algnt = SAM_Alignment.from_SAM_line( line ) ~/python/lib/python2.7/site-packages/HTSeq-0.5.3p1-py2.7-linux- x86_64.egg/HTSeq/__init__.py:592: UserWarning: Read GA2-EAS337_0017_FC:1:8:11202:16260#0 claims to have an aligned mate which could not be found. (Is the SAM file properly sorted?) "which could not be found. (Is the SAM file properly sorted?)" ) but I can found GA2-EAS337_0017_FC:1:8:11202:16260#0 mate in the data, as show in the attachments a.sam. And the a.sam is sorted by the name (default by bwa). In htseq-count, it also have this problem. htseq-count a.sam Homo_sapiens.GRCh37.63/Homo_sapiens.GRCh37.63.gtf 100000 GFF lines processed. 200000 GFF lines processed. ... 2000000 GFF lines processed. 2064769 GFF lines processed. Warning: Malformed SAM line: RNAME != '*' although flag bit &0x0004 set Warning: Read GA2-EAS337_0017_FC:1:8:11202:16260#0 claims to have an aligned mate which could not be found. (Is the SAM file properly sorted?) 4 sam line pairs processed. Why here report 4 line pairs? In fact, there are 3 sam line pairs in a.sam. BTW: in your opinions, to do this kind of count using BWA or tophat mapping, which one is better? (Illumina pair-end human RNA-seq data) Thank you.
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HI Fabrice On 08/04/2011 05:41 PM, Fabrice Tourre wrote: > When I run python script dexseq_count.py in DEXseq. I have these error. > UserWarning: Malformed SAM line: MRNM != '*' although flag bit&0x0008 You can ignore a warning. It is due to a strange way how 'bwa' interprets the SAM format. > counts[ '_loqaqual' ] += 1 > KeyError: '_loqaqual' This looks like a typo; should read '_lowaqual'. I've corrected it in SVN. Strange that it hasn't caused trouble before; maybe I introduced the typo recently. Simon
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Simon Anders ★ 3.7k
@simon-anders-3855
Last seen 2.5 years ago
Zentrum für Molekularbiologie, Universi…
Hi On 08/04/2011 02:26 PM, Jinyan Huang wrote: > R CMD INSTALL DEXSeq_0.1.12.tar.gz > * installing to library '~/R/x86_64-pc-linux-gnu-library/2.12' > ERROR: dependency 'stringr' is not available for package 'DEXSeq' > * removing '~/R/x86_64-pc-linux-gnu-library/2.12/DEXSeq' > > sessionInfo() > R version 2.12.1 (2010-12-16) > Platform: x86_64-pc-linux-gnu (64-bit) [...] DEXSeq is not yet available in the release version of Bioconductor. You need to use the development version of R and of Bioconductor. Then, install it using 'biocLite' (see Bioconductor web site), not 'R CMD INSTALL'. Simon
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