I want to run cufflinks on BWA alignments however I keep getting this error:
Error running cufflinks. [Errno 2] No such file or directory: 'transcripts.gtf'
cufflinks v1.0.3
cufflinks -q --no-update-check -I 300000 -F 0.050000 -j 0.050000 -p 4
I have downloaded the refGene mm10 as gtf from UCSC table browser.
Anyone have an idea?
Error running cufflinks. [Errno 2] No such file or directory: 'transcripts.gtf'
cufflinks v1.0.3
cufflinks -q --no-update-check -I 300000 -F 0.050000 -j 0.050000 -p 4
I have downloaded the refGene mm10 as gtf from UCSC table browser.
Anyone have an idea?