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? Thanks, Cam [[alternative HTML version deleted]]

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

On 05/06/13 02:07, Chunjiang He wrote: > 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? Yes.