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Old 05-08-2012, 11:02 PM   #1
paula123
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Default 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.
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Old 05-08-2012, 11:21 PM   #2
colindaven
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Have a look at the samtools software package for this . Samtools idxstats / flagstat should help out.
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