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

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

sequencing
• 6,842 views • link
updated by WouterDeCoster WouterDeCoster • written by Cindy • Cindy

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

Best

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written by Titus Titus

1 answer

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

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written by WouterDeCoster WouterDeCoster

Thanks. I have used samtools to remap.

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written by Cindy • Cindy

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