Hi
I ran tophat with replicate samples for a control & treated sample, then ran cufflinks, followed by cuffmerge. I provided a GTF file to cuffmerge.
When I attempt to run cuffdiff I get the following error:
You are using Cufflinks v1.3.0, which is the most recent release.
Error: cannot open reference GTF file –L for reading
my command line is:
cuffdiff -o diff_out -b genome.fa –L C,T -u merged_asm/merged.gtf ./C1/accepted_hits.bam,./C2/accepted_hits.bam ./T1/accepted_hits.bam,./T2/accepted_hits.bam
Any suggestions?
thanks
Charles
I ran tophat with replicate samples for a control & treated sample, then ran cufflinks, followed by cuffmerge. I provided a GTF file to cuffmerge.
When I attempt to run cuffdiff I get the following error:
You are using Cufflinks v1.3.0, which is the most recent release.
Error: cannot open reference GTF file –L for reading
my command line is:
cuffdiff -o diff_out -b genome.fa –L C,T -u merged_asm/merged.gtf ./C1/accepted_hits.bam,./C2/accepted_hits.bam ./T1/accepted_hits.bam,./T2/accepted_hits.bam
Any suggestions?
thanks
Charles
Comment