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Old 05-09-2012, 12:02 AM   #1
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Default TMAP alignment statistics

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.
paula123 is offline   Reply With Quote
Old 05-09-2012, 12:21 AM   #2
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Have a look at the samtools software package for this . Samtools idxstats / flagstat should help out.
colindaven is offline   Reply With Quote

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