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  • Does accepted_hits.bam include unmapped.bam reads

    Does the accepted_hits.bam file generated by Tophat2 include those placed in unmapped.bam.

    I ask because when I run:
    samtools view accepted_hits.bam | cut -f1 | sort | uniq | wc -l

    And then run:
    cat sample.fq | wc -l
    <result from previous command> / 4

    The two values are exactly the same!

  • #2
    The short answer: nope
    Marco

    Comment


    • #3
      Originally posted by marcowanger View Post
      The short answer: nope
      I'm interested in the long answer. It is too much of a coincidence that these numbers are the same. I'm wanting to get a percentage of mapped reads and unmapped reads of the total number of reads.

      Thanks

      Comment

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