Merge The Sam Files For Dexseq

Question: Merge The Sam Files For Dexseq

5.8 years ago by

camelbbs • 650

China

camelbbs • 650 wrote:

I have RNAseq data for one sample, with two technical replicates. As I know, I need to merge them to get the gene or exon counts.

Now I get the sam files from the two techinical replicates, can I merge the sam files as: cat 1.sam 2.sam > merged.sam and then sort -k1,1 -k2,2 merged.sam?

I want to use the merged sam file for dexseq_counts.py. My sam files don't have header.. Anyone has an idea about that? Thanks..

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modified 5.8 years ago by venkateshr89 • 690 • written 5.8 years ago by camelbbs • 650

5.8 years ago by

venkateshr89 • 690

United States

venkateshr89 • 690 wrote:

You can just merge the SAM files by "cat" function. Btw I don't understand why you have sam files. It will just fill up your hard drive. Downstream analysis in DEXSeq can accept BAM files. Also I wonder why your sam files did not have headers. Please try using IGV browser to see if your alignment looks fine before DEXSeq. Since you will be wasting lot of time if the counts generated by DEXSeq are wrong.

ADD COMMENT • link written 5.8 years ago by venkateshr89 • 690

I need to count the reads on exons by dexseq_counts.py, that need sam files, right?

ADD REPLY • link modified 5.8 years ago • written 5.8 years ago by camelbbs • 650

yes, If you are using DEXSeq_count.py to generate the count files. I always use HTSeq_count.py. I don't see a point why you should not DEXSeq_count.py. You are in right path. Good luck

ADD REPLY • link written 5.8 years ago by venkateshr89 • 690

5.8 years ago by

Devon Ryan ♦ 88k

Freiburg, Germany

Devon Ryan ♦ 88k wrote:

If they don't have headers, then just concatenating them will work fine. I wonder why they don't have headers though, that's odd. The sort should name sort them correctly. BTW, with many mappers, you can just supply a list of technical replicate files separated by a comma and the mapper will just output a single file with all of the reads (just to save you a step).

ADD COMMENT • link written 5.8 years ago by Devon Ryan ♦ 88k

My technical replicates are single-end and paired-end, so I think I can't merge them before I map them.

ADD REPLY • link written 5.8 years ago by camelbbs • 650

Ah, in that case yes.

ADD REPLY • link written 5.8 years ago by Devon Ryan ♦ 88k

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