Hi, Yan The htseq_bams_to_count_matrix tool in the test toolshed might be worth a try - it creates tabular count matrices from any number of individual sample bam/sam files (it is NOT read group aware!). Each row contains the count for that contig for each sample. It uses HTSeq code and you supply your favourite gene model as a GTF file for defining the regions to count and how to amalgamate - eg count reads overlapping exons and sum those into total counts for each gene. Please give it a try. Install from the admin interface and let me know how you get on. There's a companion tool differential_count_models also in the test toolshed that includes edgeR, DESeq2 and VOOM from Bioconductor - it runs 1 or 2 way GLMs using the count matrices generated by the htseq tool - be warned that it takes a long time to install everything so be patient and allow 20 minutes or so for the installation to finish because it compiles and installs R 3.0.1 and Bioconductor packages.
Suggestions for improvement or bug reports always welcomed. Good luck. On Thu, Aug 22, 2013 at 3:35 PM, Yan He <yanh...@hotmail.com> wrote: > Hi Jen and other galaxy-users,**** > > ** ** > > I am analyzing our RNA-seq data. First, I mapped the RNA-seq data to the > reference genome. I am wondering if there is a tool that could count the > number of reads that mapped to each gene. That’s important information for > my subsequent analysis. Any reply is highly appreciated! Thanks,**** > > ** ** > > Yan**** > > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ >
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
