[BioC] a question in merging sam files for DEXSeq

[Steve Lianoglou]

Hi,

On Tue, Jun 4, 2013 at 5:07 PM, Chunjiang He <camelbbs at gmail.com> wrote:
> Hi all,
>
> I want to ask a question about using DEXSeq.
>
> I have two technical replicates for one sample and I need to merge them to
> get the exon counts.
>
> I've mapped them and get the sam files, can I just merge them as :
>
> cat 1.sam 2.sam > merged.sam
>
> and then sort it: sort -k1,1 -k2,2n merged.sam > merged.sorted.sam
>
> Then I use this merged.sorted.sam on dexseq_counts.py to get the exon
> counts.
>
> Is that Ok for my process?

Have you tried it?

-steve

--
Steve Lianoglou
Computational Biologist
Bioinformatics and Computational Biology
Genentech