[BioC] Where is DEXSeq bioconductor package?

[Sean Davis]

On Thu, Aug 4, 2011 at 12:11 PM, Fabrice Tourre <fabrice.ciup at gmail.com> wrote:
> 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?

I believe that is correct, yes, for the sequence itself; this is not
specific to BWA as this is how the SAM format works.  Sorry for my
confusion in your last email.

Sean


> 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
>>
>
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