Question: How to merge multiple bam files into single bam file
0
gravatar for Bioinfonext
17 months ago by
Bioinfonext100
Korea
Bioinfonext100 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 • 1.8k views
ADD COMMENTlink modified 17 months ago by finswimmer4.5k • written 17 months ago by Bioinfonext100

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 17 months ago by WouterDeCoster31k
3
gravatar for finswimmer
17 months ago by
finswimmer4.5k
Germany
finswimmer4.5k wrote:

Hello,

samtools merge can do this.

fin swimmer

ADD COMMENTlink written 17 months ago by finswimmer4.5k

Thank you very much!

ADD REPLYlink written 17 months ago by Bioinfonext100

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

ADD REPLYlink written 17 months ago by WouterDeCoster31k

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 17 months ago by Bioinfonext100

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 17 months ago by WouterDeCoster31k
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