How to search reads with Bowtie ?

[KYR]

We did an alignment with BWA and have 4 BAM files. How can I filter only mt reads with Bowtie ?

[dariober]

Do you have any particular reason to use bowtie for this task? If not, I would use samtools as something like:

samtools index myaln.bam
samtools view -b myaln.bam chrM > myaln.chrM.bam

Best

Dario

[KYR]

Thanks! Yeah actually samtools is much more faster than Bowtie. I wanted to do a denovo alignment with Bowtie after selecting a few reads of the mitochondrial chromosomes, so I thought that I needed to use the same software to get the same file format.

Thanks for your answer!