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
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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