How to search reads with Bowtie ?
We did an alignment with BWA and have 4 BAM files. How can I filter only mt reads with Bowtie ?
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Do you have any particular reason to use bowtie for this task? If not, I would use samtools as something like:
BestCode:samtools index myaln.bam samtools view -b myaln.bam chrM > myaln.chrM.bam
Dario -
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!Comment
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