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Old 02-14-2010, 05:26 PM   #1
Location: Maryland

Join Date: Dec 2009
Posts: 15
Default Cufflinks

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?


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Old 02-15-2010, 04:58 AM   #2
Thomas Doktor
Senior Member
Location: University of Southern Denmark (SDU), Denmark

Join Date: Apr 2009
Posts: 105

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

You should check out this thread:
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