How to split both bam files and annotation files as per chromosome number?

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5.0 years ago

Glory Basumata ▴ 140

Hi All,

I am working with a large output bam files generated from the STAR aligner. The alignment is done with hg38. I would like to split these bam files to the region of interest, for instance, chromosome number or coordinates so that I could reduce the computational power. Furthermore, I would also like to do the same with the human gene annotation file- split by their chromosome number. After splitting, I would take these split files and do a quick analysis. I believe there is a tool to do that but I'm not sure which one works the best. Could someone please point me to a specific solution to this problem? Thanks!

split bam sam chr annotation • 1.3k views

ADD COMMENT • link 5.0 years ago by Glory Basumata ▴ 140

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How To Split A Bam File By Chromosome
How Can I Split Bam Into Chromosome (In A Loop) Using Samtools?

For your annotation file (use @ATPoint's version):
Extract gff of a particular chromosome

ADD REPLY • link 5.0 years ago by GenoMax 141k

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Thanks for the quick response genomax. I'll check it out now and get back. Cheers!

ADD REPLY • link 5.0 years ago by Glory Basumata ▴ 140

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