I encountered some problem when running cufflinks 2.2.1 on some sequencing data with very high coverage. When run with default setting --max-bundle-frags 1000000 , the locus with high abundance is not present in the transcripts.gtf and not in skipped.gtf either. When run with --max-bundle-frags 10000000 , the locus is reported in transcripts.gtf and the estimated absolute depth of read coverage across the whole transcript is ~55000 . The manual states that loci skipped due to --max-bundle-frags limit will be listed in skipped.gtf .
Has anyone experienced this issue? Hope it can be fixed soon if it's indeed an unexpected behavior of cufflinks.
I encountered some problem when running cufflinks 2.2.1 on some sequencing data with very high coverage. When run with default setting --max-bundle-frags 1000000 , the locus with high abundance is not present in the transcripts.gtf and not in skipped.gtf either. When run with --max-bundle-frags 10000000 , the locus is reported in transcripts.gtf and the estimated absolute depth of read coverage across the whole transcript is ~55000 . The manual states that loci skipped due to --max-bundle-frags limit will be listed in skipped.gtf .
Has anyone experienced this issue? Hope it can be fixed soon if it's indeed an unexpected behavior of cufflinks.