Question: How to merge multiple bam files into single bam file
0
gravatar for Bioinfonext
21 months ago by
Bioinfonext120
Korea
Bioinfonext120 wrote:

I mapped 30 pair end reads file separately to the genome. now please suggest how to merge these 30 mapped bam files to generate single bam file to do genome guided assembly.

rna-seq • 2.4k views
ADD COMMENTlink modified 21 months ago by finswimmer8.0k • written 21 months ago by Bioinfonext120

This question could have been solved easily by a quick google search e.g. searching for 'merge bam files'. Please first try to find a solution on your own before asking questions.

ADD REPLYlink written 21 months ago by WouterDeCoster35k
3
gravatar for finswimmer
21 months ago by
finswimmer8.0k
Germany
finswimmer8.0k wrote:

Hello,

samtools merge can do this.

fin swimmer

ADD COMMENTlink written 21 months ago by finswimmer8.0k

Thank you very much!

ADD REPLYlink written 21 months ago by Bioinfonext120

If this answer resolved your question you should mark it as "accepted".

ADD REPLYlink written 21 months ago by WouterDeCoster35k

After merging all bam file into single bam file using smatools merge. Do I also sort the merge bam file to do genome guided assembly using StingTie?

ADD REPLYlink written 21 months ago by Bioinfonext120

This question could have been solved easily by reading the samtools specifications. Searching google for 'samtools merge' brought me on this page on which the answer is rapidly found in the paragraph discussing samtools merge. Please first try to find a solution on your own before asking questions.

ADD REPLYlink written 21 months ago by WouterDeCoster35k
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