I'm working on Cloudman doing RNASeq transcriptome analysis. I've made BAM file using TopHat2 and RefSeq mm10 gtf file for Junctions.
I'm now trying to Run these through DESeq2 for differential expression analysis, using the exact same gtf file. Right off the bat it fails, giving me this error:
/mnt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/vipints/deseq_hts/cec4b4fb30be/deseq_hts/deseq-hts_2.0/galaxy/./../src/deseq2-hts.sh: line 61: /samtools: No such file or directory
Any thoughts? I'm not sure which 'file' or 'directory' it's referring to