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Old 12-30-2009, 01:11 PM   #1
bioinfosm
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Default sam output from novoalign

Hi,

I used novoalign to report Random hit for multiply mapping reads in SAM output format. How would I be able to differentiate a mapped read as multiply mapping or uniquely mapping?

It might be a way to interpret from the samtools flag (http://samtools.sourceforge.net/samtools.shtml)

From my output in sam format, the flag in second field is 0, 4 or 16
$ cut -f2 novo.out | sort | uniq -c
27431 0
27539 16
396381 4
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Old 01-06-2010, 02:04 PM   #2
bioinfosm
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Default

It belongs here actually
http://seqanswers.com/forums/showthread.php?t=2301
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