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@dpryan.com> wrote:

> It would be helpful if you reported the actual error messages.
>
> ____________________________________________
> Devon Ryan, Ph.D.
> Email: dpryan@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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> > Bioconductor@r-project.org
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> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>

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