Question: How to map the reads from a Bam file to another reference genome????
0
gravatar for Cindy
2.4 years ago by
Cindy20
Cindy20 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 • 2.2k views
ADD COMMENTlink modified 2.4 years ago by WouterDeCoster41k • written 2.4 years ago by Cindy20
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 2.4 years ago by Titus900
3
gravatar for WouterDeCoster
2.4 years ago by
Belgium
WouterDeCoster41k wrote:

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

ADD COMMENTlink written 2.4 years ago by WouterDeCoster41k

Thanks. I have used samtools to remap.

ADD REPLYlink written 2.4 years ago by Cindy20
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