[BioC] Recommended gene model for DESeq

[Nicolas Delhomme]

Hi Simon,

These are good sanity checks indeed. I'll add that to my TODO.

Nico

---------------------------------------------------------------
Nicolas Delhomme

Genome Biology Computational Support

European Molecular Biology Laboratory

Tel: +49 6221 387 8310
Email: nicolas.delhomme at embl.de
Meyerhofstrasse 1 - Postfach 10.2209
69102 Heidelberg, Germany
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On 7 Apr 2012, at 16:30, Simon Anders wrote:

> Hi Nico
> 
> On 2012-04-07 12:36, Nicolas Delhomme wrote:
>> Another word of caution here: I do not check the unicity of the reads
>> in the bam file. I expect the user to know enough about the aligner
>> (s)he is using for his/her application to decide on that. From the
>> literature it seems that people only retains uniquely mapped reads
>> (for most applications). I could add a sanity check for that.
> 
> I've added to htseq-count a check that a read gets skipped if it has tag "NH:i:n" with n>1. However, not all aligner use the NH tag properly, so this is not a full solution. Another possibility is to discard everything with mapping quality below 10, because non-uniquly mapped reads should have a MAPQ<3.
> 
> How is life in Umeå?
> 
>  Simon
> 
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