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gpertea / stringtie

Transcript assembly and quantification for RNA-Seq
MIT License
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Error: no transcripts were found in input file #150

Closed hsmith9002 closed 7 years ago

hsmith9002 commented 7 years ago

I am trying to perform stringtie --merge:

The contents of the folder where I want to merge are :

ACI-SegHsd-brain_ST.gtf F344-Ncl-brain_ST.gtf SR-JrHsd1-brain_ST.gtf Cop-CrCrl_brain_ST.gtf LEW-Crl-brain_ST.gtf SS-JrHsd-brain_ST.gtf Dark-Agouti-brain_ST.gtf SHRSP-Crl-brain_ST.gtf WKY-NCrl-brain_ST.gtf

and the mergelist.txt looks like :

ACI-SegHsd-brain_ST.gtf Cop-CrCrl_brain_ST.gtf Dark-Agouti-brain_ST.gtf F344-Ncl-brain_ST.gtf LEW-Crl-brain_ST.gtf SHRSP-Crl-brain_ST.gtf SR-JrHsd1-brain_ST.gtf SS-JrHsd-brain_ST.gtf WKY-NCrl-brain_ST.gtf

Everything is identical, and I am performing the merge inside the folder where the .gtf files are with this command:

stringtie --merge -m 0 -T 0 -F 0 -p 8 ~/Saba_Lab/RNA-Seq/HRDP/Transcript_Reconstruction/index/Rattus_norvegicus.Rnor_6.0.90.cleaned.gtf -o ~/Saba_Lab/RNA-Seq/HRDP/Transcript_Reconstruction/Brain/StringTie_Merged_Brain ~/Saba_Lab/RNA-Seq/HRDP/Transcript_Reconstruction/mergelist_brain.txt.

I have inspected each individual sample .gtf, and they do indeed have transcripts in them. I have had no trouble with this step before, but I cannot figure out what is going wrong this time. Is there perhaps a problem with the file names?

Thank you

hsmith9002 commented 7 years ago

I figured this out. I was just missing the -G.