Question: How to merge multiple bam files into single bam file
0
gravatar for nabiyogesh
4 months ago by
nabiyogesh70
South Korea
nabiyogesh70 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 • 275 views
ADD COMMENTlink modified 4 months ago by finswimmer280 • written 4 months ago by nabiyogesh70

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 4 months ago by WouterDeCoster20k
3
gravatar for finswimmer
4 months ago by
finswimmer280
Germany
finswimmer280 wrote:

Hello,

samtools merge can do this.

fin swimmer

ADD COMMENTlink written 4 months ago by finswimmer280

Thank you very much!

ADD REPLYlink written 4 months ago by nabiyogesh70

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

ADD REPLYlink written 4 months ago by WouterDeCoster20k

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 4 months ago by nabiyogesh70

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 4 months ago by WouterDeCoster20k
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