I used cufflinks to estimate gene expression in a gtf file, however, one sample could not pass one loci, always stopped there (all the other samples are fine); the command i used is as following:
cufflinks -G XXX.gtf YYY.bam
the error information is as following:
You are using Cufflinks v1.1.0, which is the most recent release.
[18:37:04] Loading reference annotation.
[18:37:04] Inspecting reads and determining fragment length distribution.
> Processing Locus chr21:9825743-9826389 [************* ] 52%
this lasts for ever and I then changed --max-bundle-frags to 2000000, but still stoppped here; after that I went to gtf file to find the loci and deleted this loci, now it stopped in another loci, what should I do? delete another loci? helps please!!!
cufflinks -G XXX.gtf YYY.bam
the error information is as following:
You are using Cufflinks v1.1.0, which is the most recent release.
[18:37:04] Loading reference annotation.
[18:37:04] Inspecting reads and determining fragment length distribution.
> Processing Locus chr21:9825743-9826389 [************* ] 52%
this lasts for ever and I then changed --max-bundle-frags to 2000000, but still stoppped here; after that I went to gtf file to find the loci and deleted this loci, now it stopped in another loci, what should I do? delete another loci? helps please!!!
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