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Old 01-27-2016, 03:37 AM   #4
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Location: Vienna

Join Date: Oct 2011
Posts: 123

Hi Ivygreen,
I'd run cufflinks on one/two sample first, there you'll maybe get a more detailed report. Check also if the bam-files are indexed (e.g. samtools index 008_F0/accepted_hits.bam) and if the chromosome names are the same in the alignment and the GTF file.
Michael.Ante is offline   Reply With Quote