Question: What is the best way to re-align a .bam file?
0
gravatar for tech
3 months ago by
tech0
tech0 wrote:

I need to know exactly what reference genome was used to align a file, so I am looking for a way to de-align and re-align an existing .bam.

Could you suggest a correct way to do this? Is my original approach of going from .bam -> .fastq -> .sam -> .bam feasible?

Is there any loss of information?

P.S. At the moment I am using samtools bam2fq.

samtools bam fastq fasta • 152 views
ADD COMMENTlink modified 3 months ago by WouterDeCoster44k • written 3 months ago by tech0
1

I used ngs-bits BamToFastq, but bedtools bamToFastq should work just as good for .bam -> .fastq.

I would not expect a loss of information unless you've filtered out unmapped reads from your bam files. Also hard clipping can create a problem - but more knowledgable people may answer better.

ADD REPLYlink written 3 months ago by German.M.Demidov1.8k
4
gravatar for WouterDeCoster
3 months ago by
Belgium
WouterDeCoster44k wrote:

Bazam has been developed precisely for this purpose.

ADD COMMENTlink written 3 months ago by WouterDeCoster44k

Just tested bazam and it works great. Thanks a lot!

ADD REPLYlink written 3 months ago by tech0
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