How to map the reads from a Bam file to another reference genome????

Question

[Cindy]

Dear all,

I have got BAM files of mitochondrial DNA sequencing, which were aligned to mtDNA reference genome. Now I want to look at whether those mapped reads also have some overlap with nuclear genome. What should I do? I have extracted mapped reads from bam files, should I just use bwa to align to nuclear reference genome?

Thanks

Cindy

[Titus]

Hi Cindy, If you have extract a fastq yes you can simply realign your reads against your new reference using bwa :)

Best

Answer 1

[WouterDeCoster]

You can convert the bam file back to fastq (samtools fastq), and use that for mapping just like usual mapping.

[Cindy]

Thanks. I have used samtools to remap.