Hi,
after cufflinks generates tnp1/transcripts.gtf tmp2/transcripts.gtf (attached: tmp_gtf.zip)
I run cuffcompare (attachted: combined_gtf.zip) to generate a .combined.gtf from both of these .gtf files by
> cuffcompare -p 5 tmp1/transcripts.gtf tmp2/trascripts.gtf
> less stdout.combined.gtf
"stdout.combined.gtf" may be a binary file. See it anyway?
column 7, which should be "strand" from GTF, is presented by a weired "^@" character.
Currently, I replace this column by "." .
I am wondering if anybody met the same problem before. Maybe Cole can help to explain?!
tmp_gtf.zip
combined_gtf.zip
after cufflinks generates tnp1/transcripts.gtf tmp2/transcripts.gtf (attached: tmp_gtf.zip)
I run cuffcompare (attachted: combined_gtf.zip) to generate a .combined.gtf from both of these .gtf files by
> cuffcompare -p 5 tmp1/transcripts.gtf tmp2/trascripts.gtf
> less stdout.combined.gtf
"stdout.combined.gtf" may be a binary file. See it anyway?
column 7, which should be "strand" from GTF, is presented by a weired "^@" character.
Currently, I replace this column by "." .
I am wondering if anybody met the same problem before. Maybe Cole can help to explain?!
tmp_gtf.zip
combined_gtf.zip
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