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  • 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 ?

  • #2
    Do you have any particular reason to use bowtie for this task? If not, I would use samtools as something like:

    Code:
    samtools index myaln.bam
    samtools view -b myaln.bam chrM > myaln.chrM.bam
    Best

    Dario

    Comment


    • #3
      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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