How to merge multiple bam files into single bam file

Question

[Bioinfonext]

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.

[WouterDeCoster]

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.

Answer 1

[finswimmer]

Hello,

samtools merge can do this.

fin swimmer

[Bioinfonext]

Thank you very much!

[WouterDeCoster]

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

[Bioinfonext]

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?

[WouterDeCoster]

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.