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Old 01-24-2013, 11:51 AM   #1
Junior Member
Location: USA

Join Date: Jan 2013
Posts: 2
Default newbie edgeR

I am new to next Gen sequencing and R. We got the .bam files from the core and my boss wants me to find the differential expression of the genes in 2 time points. So I was wondering is it possible to do edgeR from the .bam or the rpkm files. If so can you please forward me to that website.
Thank you
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Old 01-25-2013, 01:00 AM   #2
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

edgeR doesn't use the RPKM values as input, but rather the raw counts per gene. The normal work-flow is to run htseq-count on the various BAM files and then use the outputs in edgeR (or DESeq or one of the many other analysis programs). To do that, just invoke something like the following for each BAM file:

samtools view SOMEFILE.BAM | htseq-count - GTF > counts.txt
where SOMEFILE.BAM is a BAM file and GTF is whatever annotation GTF is appropriate for your experiments. If all of your BAM files are in the same directory, remember to change the name of counts.txt with every file. You may also need to change the options used with htseq-count (often -m or -i).

Also, there are a few lines of summary information printed at the end of the htseq-count input, you can remove those now in a text editor, or do so later in R (whatever you prefer).
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