[BioC] DEXSeq update
dpryan at dpryan.com
Sun Oct 6 23:29:42 CEST 2013
It would be helpful if you reported the actual error messages.
Devon Ryan, Ph.D.
Email: dpryan at dpryan.com
Tel: +49 (0)178 298-6067
Molecular and Cellular Cognition Lab
German Centre for Neurodegenerative Diseases (DZNE)
53175 Bonn, Germany
On Oct 6, 2013, at 10:51 PM, Margaret Linan wrote:
> Hi Simon,
> It appears that one of my regular unsorted SAM files is truncated.
> Though the sort works fine and samtools view does not detect truncation
> in my file.sam.bam, I still get error messages after attempting to generate
> counts files.
> samtools view -h file.sam.bam | python dexseq_count.py file.gff -
> Do you think that the truncation may be behind the problems?
> I can't check the structure of my SAM.BAM file because its all symbols,
> though when I use samtools view, the contents runs across the screen, and I
> am unable to pinpoint any irregularity.
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