Dexseq package: dexseq_count error message and warnings
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capricy gao ▴ 230
@capricy-gao-5298
Last seen 9.6 years ago
I am planning to compare the exon usage between samples. This is my first time to use Dexdeq. The problem came when I tried to use dexseq_count.py. My RNAseq data was mapped using tophat, then  the bam file was samtools sorted with -n (by name) , samtools converted the sorted bam into sam I followed the online manual (http://www.bioconductor.org/packages/2.1 3/bioc/vignettes/DEXSeq/inst/doc/DEXSeq.pdf) to fun dexseq_count: /R/x86_64-pc-linux-gnu- library/2.15/DEXSeq/python_scripts/dexseq_count.py  -r name -p yes -s no HTseqFormat_flatterned.gff sample.sam sample.exonCounts the first error message was :  no such option: -r Could anybody let me know why? On page 5 of the manual, it clearly says this option should be included I then deleted this option and a lot of warnings came out:  claims to have an aligned mate which could not be found. (Is the SAM file properly sorted?) These warnings might came up because when I ran tophat, I did not specify the correct " expected (mean) inner distance between mate pairs". I wonder if I could just remove -p option and treat the file like non paired-end data? Thanks a lot:) [[alternative HTML version deleted]]
RNASeq RNASeq • 1.8k views
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Alejandro Reyes ★ 1.9k
@alejandro-reyes-5124
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Novartis Institutes for BioMedical Rese…
Dear Capricy Gao, Let me know if I am wrong, but it sounds like you are using a vignette found by google that does not match with the version of DEXSeq that you are using. What version of DEXSeq do you have installed? The "-r" option was included from DEXSeq 1.7.8, so first make sure that you have this or a newer version installed. Best regards, Alejandro > I am planning to compare the exon usage between samples. This is my first time to use Dexdeq. The problem came when I tried to use dexseq_count.py. > > > My RNAseq data was mapped using tophat, then the bam file was samtools sorted with -n (by name) , samtools converted the sorted bam into sam > > I followed the online manual (http://www.bioconductor.org/packages/2 .13/bioc/vignettes/DEXSeq/inst/doc/DEXSeq.pdf) to fun dexseq_count: > > /R/x86_64-pc-linux-gnu- library/2.15/DEXSeq/python_scripts/dexseq_count.py -r name -p yes -s no HTseqFormat_flatterned.gff sample.sam sample.exonCounts > > > the first error message was : no such option: -r > > Could anybody let me know why? On page 5 of the manual, it clearly says this option should be included > > > I then deleted this option and a lot of warnings came out: claims to have an aligned mate which could not be found. (Is the SAM file properly sorted?) > > These warnings might came up because when I ran tophat, I did not specify the correct " expected (mean) inner distance between mate pairs". I wonder if I could just remove -p option and treat the file like non paired-end data? > > > Thanks a lot:) > > [[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 [[alternative HTML version deleted]]
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Oh, you are right. Here is the my session information. --------------- > sessionInfo()R version 2.15.2 (2012-10-26) Platform: x86_64-pc-linux-gnu (64-bit) other attached packages: [1] edgeR_3.0.8        limma_3.14.4       DEXSeq_1.4.0 Biobase_2.16.0 [5] BiocGenerics_0.4.0 ------------------- But I downloaded it yesterday... How should I change it? And do you have any idea about my warning messages? Thanks a lot for your help:) On Thursday, November 7, 2013 12:43 AM, Alejandro Reyes <alejandro.reyes@embl.de> wrote: Dear Capricy Gao, Let me know if I am wrong, but it sounds like you are using a vignette found by google that does not match with the version of DEXSeq that you are using.  What version of DEXSeq do you have installed? The "-r" option was included from DEXSeq 1.7.8, so first make sure that you have this or a newer version installed. Best regards, Alejandro I am planning to compare the exon usage between samples. This is my first time to use Dexdeq. The problem came when I tried to use dexseq_count.py. My RNAseq data was mapped using tophat, then  the bam file was samtools sorted with -n (by name) , samtools converted the sorted bam into sam I followed the online manual (http://www.bioconduc tor.org/packages/2.13/bioc/vignettes/DEXSeq/inst/doc/DEXSeq.pdf) to fun dexseq_count: /R/x86_64-pc-linux-gnu- library/2.15/DEXSeq/python_scripts/dexseq_count.py  -r name -p yes -s no HTseqFormat_flatterned.gff sample.sam sample.exonCounts the first error message was :  no such option: -r Could anybody let me know why? On page 5 of the manual, it clearly says this option should be included I then deleted this option and a lot of warnings came out: claims to have an aligned mate which could not be found. (Is the SAM file properly sorted?) These warnings might came up because when I ran tophat, I did not specify the correct " expected (mean) inner distance between mate pairs". I wonder if I could just remove -p option and treat the file like non paired-end data? Thanks a lot:) [[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 [[alternative HTML version deleted]]
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Dear Capricy Gao, You have a very old version of R. If you are installing DEXSeq using the function "biocLite", you will have to update your R version at least to the latest release. Bests, Alejandro > Oh, you are right. Here is the my session information. > > --------------- > > sessionInfo()R version 2.15.2 (2012-10-26) > Platform: x86_64-pc-linux-gnu (64-bit) > other attached packages: > [1] edgeR_3.0.8 limma_3.14.4 DEXSeq_1.4.0 Biobase_2.16.0 > [5] BiocGenerics_0.4.0 > ------------------- > > But I downloaded it yesterday... > > How should I change it? > > And do you have any idea about my warning messages? > > Thanks a lot for your help:) > > > > > > On Thursday, November 7, 2013 12:43 AM, Alejandro Reyes > <alejandro.reyes at="" embl.de=""> wrote: > Dear Capricy Gao, > > Let me know if I am wrong, but it sounds like you are using a vignette > found by google that does not match with the version of DEXSeq that > you are using. What version of DEXSeq do you have installed? > > The "-r" option was included from DEXSeq 1.7.8, so first make sure > that you have this or a newer version installed. > > Best regards, > Alejandro > > >> I am planning to compare the exon usage between samples. This is my first time to use Dexdeq. The problem came when I tried to use dexseq_count.py. >> >> >> My RNAseq data was mapped using tophat, then the bam file was samtools sorted with -n (by name) , samtools converted the sorted bam into sam >> >> I followed the online manual (http://www.bioconductor.org/packages/ 2.13/bioc/vignettes/DEXSeq/inst/doc/DEXSeq.pdf) to fun dexseq_count: >> >> /R/x86_64-pc-linux-gnu- library/2.15/DEXSeq/python_scripts/dexseq_count.py -r name -p yes -s no HTseqFormat_flatterned.gff sample.sam sample.exonCounts >> >> >> the first error message was : no such option: -r >> >> Could anybody let me know why? On page 5 of the manual, it clearly says this option should be included >> >> >> I then deleted this option and a lot of warnings came out: claims to have an aligned mate which could not be found. (Is the SAM file properly sorted?) >> >> These warnings might came up because when I ran tophat, I did not specify the correct " expected (mean) inner distance between mate pairs". I wonder if I could just remove -p option and treat the file like non paired-end data? >> >> >> Thanks a lot:) >> >> [[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.inf ormatics.conductor > > >
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The problem is our server updates R once a year, I think. How does it affect the results? On Thursday, November 7, 2013 9:10 AM, Alejandro Reyes <alejandro.reyes@embl.de> wrote: Dear Capricy Gao, You have a very old version of R. If you are installing DEXSeq using the function "biocLite", you will have to update your R version at least to the latest release. Bests, Alejandro > Oh, you are right. Here is the my session information. > > --------------- > > sessionInfo()R version 2.15.2 (2012-10-26) > Platform: x86_64-pc-linux-gnu (64-bit) > other attached packages: > [1] edgeR_3.0.8        limma_3.14.4      DEXSeq_1.4.0 Biobase_2.16.0 > [5] BiocGenerics_0.4.0 > ------------------- > > But I downloaded it yesterday... > > How should I change it? > > And do you have any idea about my warning messages? > > Thanks a lot for your help:) > > > > > > On Thursday, November 7, 2013 12:43 AM, Alejandro Reyes > <alejandro.reyes@embl.de> wrote: > Dear Capricy Gao, > > Let me know if I am wrong, but it sounds like you are using a vignette > found by google that does not match with the version of DEXSeq that > you are using.  What version of DEXSeq do you have installed? > > The "-r" option was included from DEXSeq 1.7.8, so first make sure > that you have this or a newer version installed. > > Best regards, > Alejandro > > >> I am planning to compare the exon usage between samples. This is my first time to use Dexdeq. The problem came when I tried to use dexseq_count.py. >> >> >> My RNAseq data was mapped using tophat, then  the bam file was samtools sorted with -n (by name) , samtools converted the sorted bam into sam >> >> I followed the online manual (http://www.bioconductor.org/packages/ 2.13/bioc/vignettes/DEXSeq/inst/doc/DEXSeq.pdf) to fun dexseq_count: >> >> /R/x86_64-pc-linux-gnu- library/2.15/DEXSeq/python_scripts/dexseq_count.py  -r name -p yes -s no HTseqFormat_flatterned.gff sample.sam sample.exonCounts >> >> >> the first error message was :  no such option: -r >> >> Could anybody let me know why? On page 5 of the manual, it clearly says this option should be included >> >> >> I then deleted this option and a lot of warnings came out:  claims to have an aligned mate which could not be found. (Is the SAM file properly sorted?) >> >> These warnings might came up because when I ran tophat, I did not specify the correct " expected (mean) inner distance between mate pairs". I wonder if I could just remove -p option and treat the file like non paired-end data? >> >> >> Thanks a lot:) >> >>     [[alternative HTML version deleted]] >> >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org  <mailto:bioconductor@r-project.org> >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives:http://news.gmane.org/gmane.science.biology.inf ormatics.conductor > > > [[alternative HTML version deleted]]
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Hi On 09/11/13 07:08, capricy gao wrote: > The problem is our server updates R once a year, I think. > > How does it affect the results? Well, without the '-r' option you cannot switch of gene aggregation, which may be inconvenient. Also, you may encounter bugs which have already been fixed. Bioinformatics is a fast moving field, and you have to do an effort to stay up to date and make sure you always work with current versions of tools. Specifically, for the Bioconductor project, it is strongly advised to not work with an outdated R version. Better talk to your sysadmin and ask him/her to update R more frequently. Simon
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On Sat, Nov 9, 2013 at 8:34 AM, Simon Anders <anders@embl.de> wrote: > Hi > > On 09/11/13 07:08, capricy gao wrote: > >> The problem is our server updates R once a year, I think. >> >> How does it affect the results? >> > > Well, without the '-r' option you cannot switch of gene aggregation, which > may be inconvenient. Also, you may encounter bugs which have already been > fixed. > > Bioinformatics is a fast moving field, and you have to do an effort to > stay up to date and make sure you always work with current versions of > tools. Specifically, for the Bioconductor project, it is strongly advised > to not work with an outdated R version. > > Better talk to your sysadmin and ask him/her to update R more frequently. > An alternative is to install your own R in your home directory. No sysadmin support is necessary to do so and it really isn't that hard (most of the time). Sean [[alternative HTML version deleted]]
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I am also bit confused that this count step is outside R according to the Dexseq manual. I checked the python script, does it request R environment? Maybe I am wrong... On Saturday, November 9, 2013 7:40 AM, Sean Davis <sdavis2@mail.nih.gov> wrote: On Sat, Nov 9, 2013 at 8:34 AM, Simon Anders <anders@embl.de> wrote: > Hi > > On 09/11/13 07:08, capricy gao wrote: > >> The problem is our server updates R once a year, I think. >> >> How does it affect the results? >> > > Well, without the '-r' option you cannot switch of gene aggregation, which > may be inconvenient. Also, you may encounter bugs which have already been > fixed. > > Bioinformatics is a fast moving field, and you have to do an effort to > stay up to date and make sure you always work with current versions of > tools. Specifically, for the Bioconductor project, it is strongly advised > to not work with an outdated R version. > > Better talk to your sysadmin and ask him/her to update R more frequently. > An alternative is to install your own R in your home directory.  No sysadmin support is necessary to do so and it really isn't that hard (most of the time). Sean     [[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 [[alternative HTML version deleted]]
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Dear Capricy, The python scripts does not require an R environment. If you install an updated version of R and DEXSeq, you will find an example of how to do this preprocessing steps within R in the Appendix section. Best regards, Alejandro > > > I am also bit confused that this count step is outside R according to > the Dexseq manual. I checked the python script, does it request R > environment? Maybe I am wrong... > > > On Saturday, November 9, 2013 7:40 AM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > > On Sat, Nov 9, 2013 at 8:34 AM, Simon Anders <anders at="" embl.de=""> wrote: > >> Hi >> >> On 09/11/13 07:08, capricy gao wrote: >> >>> The problem is our server updates R once a year, I think. >>> >>> How does it affect the results? >>> >> >> Well, without the '-r' option you cannot switch of gene aggregation, which >> may be inconvenient. Also, you may encounter bugs which have already been >> fixed. >> >> Bioinformatics is a fast moving field, and you have to do an effort to >> stay up to date and make sure you always work with current versions of >> tools. Specifically, for the Bioconductor project, it is strongly advised >> to not work with an outdated R version. >> >> Better talk to your sysadmin and ask him/her to update R more frequently. >> > > An alternative is to install your own R in your home directory. No > sysadmin support is necessary to do so and it really isn't that hard (most > of the time). > > Sean > > [[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 > [[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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