[BioC] Where is DEXSeq bioconductor package?

[Fabrice Tourre]

In bwa, the sequence presented in the sam/bam file is always the
sequence in the forward orientation relative to the reference. If it
maps to the reverse strand, then bwa reverse complements the read
sequence (and reverses the quality string) before writing it to the
sam/bam file.  Is it right?

Thank you.

On Thu, Aug 4, 2011 at 5:50 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> 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
>