[BioC] DEXSeq Paired-end analysis (new issues)

[Devon Ryan]

Hi Margaret,

It's expecting a SAM file, not a BAM file:

samtools view -h ahBC010.sam.bam | dexseq_count.py -p yes -s no hs71.gff - ahBC010.counts

Note that - specifies reading from the standard input rather than a file.

Cheers,
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 6, 2013, at 9:41 PM, Margaret Linan wrote:

> Hi Simon,
> 
> The sort code worked just fine. I also ran a diagnostic on the *.bam files
> and no error came up. But when I tried to use the sorted
> *.sam.bam  file with the dexseq_count.py program, I got the following
> messages:
> 
> 
> [mlinan at s59-14 MISC]$ python dexseq_count.py -p yes -s no hs71.gff
> ahBC010.sam.b      am  BC010.counts
> Traceback (most recent call last):
>  File "dexseq_count.py", line 132, in <module>
>    for af, ar in HTSeq.pair_SAM_alignments( HTSeq.SAM_Reader( sam_file ) ):
>  File
> "/packages/python/python-2.7.3/lib/python2.7/site-packages/HTSeq/__init__
> .py", line 610, in pair_SAM_alignments
>    for almnt in alignments:
>  File
> "/packages/python/python-2.7.3/lib/python2.7/site-packages/HTSeq/__init__
> .py", line 549, in __iter__
>    algnt = SAM_Alignment.from_SAM_line( line )
>  File "_HTSeq.pyx", line 1274, in HTSeq._HTSeq.SAM_Alignment.from_SAM_line
> (src      /_HTSeq.c:22184)
> ValueError: ('SAM line does not contain at least 11 tab-delimited fields.',
> 'lin      e 1 of file ahBC010.sam.bam')
> 
> When I opened the *sam.bam file I found the below in the first few lines.
> The entire file is a collection of random symbols with accents marks and
> numbers.
> 
> 
> ‹�����ÿ�BC�ò¥"½kAÆÇœÆ\"T
> 
> "WØîÍ×ÎÎÌ™À].’ø‘AŽÍíÜÞÆÜîåvsI!‚ h)6vÖ‚MÁ.¶"ˆþ‚] …8;"ìY
> 
> ·÷ð›gß÷}^fgËçNJ�ÔæÊë+5\EåÕÛµv’
> 
> ‚(ö35Y_½[^Õ奕q%aÈ#¸ (ǘ2F]îòãSŒÇ°W`b1
> 
> 
> É
> 
> L
> 
> ÆÚ)v
> 
> Fœº’¹¨ÀÌbÂ(¦’Ø˱D"¹œÑ‚òœ
> 
> 
> 
> Thanks,
> 
> Margaret
> 
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor