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  • paula123
    Junior Member
    • May 2012
    • 3
    #1

    TMAP alignment statistics

    Hi,
    I am using TMAP to align transcriptome data, sequenced by Ion-torrent. It is generated output file in sam format. How can I get how much read aligned and other basic required alignment statistics. Is any publication of TMAP software ?
    I am very grateful if anyone can help me.
    Tags: None
    • colindaven
      Senior Member
      • Oct 2008
      • 417
      #2
      Have a look at the samtools software package for this . Samtools idxstats / flagstat should help out.

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