This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to merge multiple bam files into single bam file

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
• 11,225 views • link
updated by finswimmer finswimmer • written by Bioinfonext Bioinfonext

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.

• 0 views • link
written by WouterDeCoster WouterDeCoster

1 answer

Hello,

samtools merge can do this.

fin swimmer

• 0 views • link
written by finswimmer finswimmer

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

• 0 views • link
written by WouterDeCoster WouterDeCoster

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?

• 0 views • link
written by Bioinfonext Bioinfonext

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.

• 0 views • link
written by WouterDeCoster WouterDeCoster

Log in to answer this question.

More posts like this