Question: How to map the reads from a Bam file to another reference genome????
0
gravatar for Cindy
3.2 years ago by
Cindy30
Cindy30 wrote:

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 • 3.0k views
ADD COMMENTlink modified 3.2 years ago by WouterDeCoster44k • written 3.2 years ago by Cindy30
1

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

Best

ADD REPLYlink written 3.2 years ago by Titus910
3
gravatar for WouterDeCoster
3.2 years ago by
Belgium
WouterDeCoster44k wrote:

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

ADD COMMENTlink written 3.2 years ago by WouterDeCoster44k

Thanks. I have used samtools to remap.

ADD REPLYlink written 3.2 years ago by Cindy30
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