Alignment Summary Metric (picard tools)

ClemBuntu

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Join Date: Dec 2014

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Alignment Summary Metric (picard tools)

10-19-2015, 11:05 PM

Hello,

That must be a silly question but I wasn't able to find any inforamtions on the web.

I used Collect Alignment Summary Metrics from picard tools on .bam file produced by TopHat wich aligned 60,685,681 paired reads (so 121,371,362 total reads) against human genome.

Collect Alignment Summary Metrics gave me the following table :

CATEGORY TOTAL_READS PF_READS
FIRST_OF_PAIR 54,396,550 54,396,550
SECOND_OF_PAIR 53,968,272 53,968,272
PAIR 108,364,822 108,364,822

I can see this tool calculates "PAIR" by summing FIRST_OF_PAIR and SECOND_OF_PAIR but that doesn't make sence because there is 428,278 reads (first of pair - second of pair) which mapped only the first in pair, in a unpaired fashion.

Can someone explain this to me please ?

Finally what I'm suppose to do to know the percentage of mapped read ?
I guess I have to do (53,968,272/60,685,681)*100 ?
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