id,summary,reporter,owner,description,type,status,priority,milestone,component,resolution,keywords,cc 1266,Run prepDE.py in the StringTie pipeline,Nicklas Nordborg,Nicklas Nordborg,"The `prepDE.py` script (http://ccb.jhu.edu/software/stringtie/index.shtml?t=manual#deseq) is part of the !StringTie package and produces files with hypothetical count for gene and transcripts. It uses information from the transcript.gtf produced by !StringTie: {{{ echo SAMPLEID stringtie/transcript.gtf > input.lst prepDE.py -i input.lst \ -g stringtie/gene_count.csv \ -t stringtie/transcript_count.csv }}} Note! We are investigating what to do with the `--length` parameter. The default value is 75, but we have used different read lengths at different times (eg. 2x50, 2x75, 2x100). The `gene_count.csv` and `transcript_count.csv` files should also be included in the release export.",task,closed,major,Reggie v4.27.4,net.sf.basedb.reggie,fixed,,