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Forum: Bioinformatics 02-03-2015, 03:31 AM
Replies: 0
Views: 1,473
Posted By fattest0828
Cufffdiff returns 0 conf_low fpkm and high conf_hi fpkm for EVERY gene

Hi all,

I am using tophat 2.0.13,cufflinks 2.2.1 to do tophat-cufflinks-cuffmerge-cuffdiff pipeline.

Here is the command I typed:

tophat -p 40 -G genes.gtf -o Testes_thout genome...
Forum: Bioinformatics 12-21-2014, 05:44 PM
Replies: 14
Views: 9,779
Posted By fattest0828
What about head(features(MyGene))? It should not...

What about head(features(MyGene))? It should not have the same error of <0 rows> (or 0-length row.names)
Forum: Bioinformatics 12-17-2014, 11:12 PM
Replies: 14
Views: 9,779
Posted By fattest0828
Hi, I had the same problem before. You need to...

Hi, I had the same problem before. You need to use readCufflinks(,gtfFile="path/to/file(the file you used for cuffdiff)"), then it will read the features in the gtf file.
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