Regarding Solexa data

ganga.jeena · 01-28-2011, 01:26 AM

What exactly does the following mean:

63_k/nohup.out

Output 285695310 out of 495475004 (57.7)% reads in gaps

352330547 out of 495475004 (71.1)% reads mapped to contigs

Regards,
Ganga Jeena

seb567 · 02-03-2011, 07:29 AM

Gaps refer to the stretches of unidentified nucleotides between contigs in your scaffolds.

Perhaps the obvious is implied -- you have reads that align in gaps.

I presume that this means that these reads don't align on contigs and therefore it is presumed that they belong in the gaps.

Could be contamination too !

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01-28-2011, 01:26 AM	#1
ganga.jeena Member Location: INDIA Join Date: Jun 2010 Posts: 15	Regarding Solexa data What exactly does the following mean: 63_k/nohup.out Output 285695310 out of 495475004 (57.7)% reads in gaps 352330547 out of 495475004 (71.1)% reads mapped to contigs Regards, Ganga Jeena

02-03-2011, 07:29 AM	#2
seb567 Senior Member Location: Québec, Canada Join Date: Jul 2008 Posts: 260	Gaps refer to the stretches of unidentified nucleotides between contigs in your scaffolds. Perhaps the obvious is implied -- you have reads that align in gaps. I presume that this means that these reads don't align on contigs and therefore it is presumed that they belong in the gaps. Could be contamination too !