Cufflinks

[hsmart]

Hi All,

I am trying use Cufflinks with output of tophat. The command is as follow:

cufflinks HTERT_tophat_accepted_hits.sam.sorted -G Homo_sapiens.GRCh37.56.gtf -L HTERT

However, Cufflinks just stops after processing bundle for all chromosomes for example,
Processing bundle [ chrY:59362092-59362127 ] with 1 non-redundant alignments

There are no data in output files. Can anyone please help me with it?

Thanks,

Rakesh

[Thomas Doktor]

I think the likely explanation is that your reference GTF file needs to be reformated.

You should check out this thread: http://seqanswers.com/forums/showthread.php?t=3972