[BioC] Where is DEXSeq bioconductor package?

[Sean Davis]

On Thu, Aug 4, 2011 at 11:41 AM, Fabrice Tourre <fabrice.ciup at gmail.com> wrote:
> When I run python script dexseq_count.py in DEXseq. I have these error.
>
> ~/bin/python/python /env/ins/home/user/bin/dexseq_count.py -p yes -s
> yes -a 10 /env/ins/home/user/rna-seq/info/DEX-63.gtf
> ~/rna-seq/exp/data/mapping/bwa/7005_4.sam test.count
>
> /env/ins/home/user/bin/python/lib/python2.7/site-packages/HTSeq-0.5.3p1-py2.7-linux-x86_64.egg/HTSeq/__init__.py:543:
> UserWarning: Malformed SAM line: MRNM != '*' although flag bit &0x0008
> set
>  algnt = SAM_Alignment.from_SAM_line( line )
> /env/ins/home/user/bin/python/lib/python2.7/site-packages/HTSeq-0.5.3p1-py2.7-linux-x86_64.egg/HTSeq/__init__.py:543:
> UserWarning: Malformed SAM line: RNAME != '*' although flag bit
> &0x0004 set
>  algnt = SAM_Alignment.from_SAM_line( line )
> Traceback (most recent call last):
>  File "/env/ins/home/user/bin/rnaseq/pipeline/dexseq_count.py", line
> 138, in <module>
>    counts[ '_loqaqual' ] += 1
> KeyError: '_loqaqual'
>
>
> Python:2.7
> HTSeq:0.5.3p1
> DEXseq:0.1.12
> Sam produced by bwa (bwa-0.5.9) against Ensembl 63 (Human, RNA-seq
> pair-end sample).
> It seems that BWA convert all the reads to forward strand, so I set -s
> yes. Is it right?

I do not think that BWA "converts" all reads to the forward strand,
although I may be misunderstanding what you mean by "converts".  The
strand information is encoded in the FLAG column.  See here:

http://samtools.sourceforge.net/SAM1.pdf

Sean