[BioC] DEXSeq update

[Devon Ryan]

That's a warning, not an error and you can likely ignore it. As Simon alluded in his earlier reply, the script expects mates in a pair to follow one another. When they don't, the warning you observed is issued. With tophat, this can occur when (1) you don't specify --no-mixed or (2) you specify --fusion-search. Tophat is known to not always produce proper flags.

Regards,
Devon

____________________________________________
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)
Ludwig-Erhard-Allee 2
53175 Bonn, Germany

On Oct 7, 2013, at 12:21 AM, Margaret Linan wrote:

> After properly sorting, using Simons method and then using the dexseq count program I get error messages
>  
> These are a sample of the error messages:
> 
> UserWarning: Read HWI-ST522:121:D0V1CACXX:8:1106:20332:74088 claims to have an aligned mate which could not be found. (Is the SAM file properly sorted?)
>   "which could not be found. (Is the SAM file properly sorted?)" )
> /packages/python/python-2.7.3/lib/python2.7/site-packages/HTSeq/__init__.py:598: UserWarning: Read HWI-ST522:121:D0V1CACXX:8:1106:21152:96414 claims to have an aligned mate which could not be found. (Is the SAM file properly sorted?)
>   "which could not be found. (Is the SAM file properly sorted?)" )
> /packages/python/python-2.7.3/lib/python2.7/site-packages/HTSeq/__init__.py:598: UserWarning: Read HWI-ST522:121:D0V1CACXX:8:1106:2563:90289 claims to have an aligned mate which could not be found. (Is the SAM file properly sorted?)
>   "which could not be found. (Is the SAM file properly sorted?)" )
> /packages/python/python-2.7.3/lib/python2.7/site-packages/HTSeq/__init__.py:598: UserWarning: Read HWI-ST522:121:D0V1CACXX:8:1106:2842:88054 claims to have an aligned mate which could not be found. (Is the SAM file properly sorted?)
>   "which could not be found. (Is the SAM file properly sorted?)" )
> /packages/python/python-2.7.3/lib/python2.7/site-packages/HTSeq/__init__.py:598: UserWarning: Read HWI-ST522:121:D0V1CACXX:8:1106:6895:17883 claims to have an aligned mate which could not be found. (Is the SAM file properly sorted?)
>   "which could not be found. (Is the SAM file properly sorted?)" )
> /packages/python/python-2.7.3/lib/python2.7/site-packages/HTSeq/__init__.py:598: UserWarning: Read HWI-ST522:121:D0V1CACXX:8:1106:7069:24372 claims to have an aligned mate which could not be found. (Is the SAM file properly sorted?)
>   "which could not be found. (Is the SAM file properly sorted?)" )
> Thanks,
> Margaret
> 
> 
> On Sun, Oct 6, 2013 at 2:29 PM, Devon Ryan <dpryan at dpryan.com> wrote:
> 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)
> Ludwig-Erhard-Allee 2
> 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 -
> > file.counts
> >
> > 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.
> >
> > Thanks,
> > Margaret
> >
> >       [[alternative HTML version deleted]]
> >
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>