Qualimap insert size result explanation

3.5 years ago by

geek_y ♦ 8.5k

geek_y ♦ 8.5k wrote:

Zero insert size means :

1. mate unmapped. (or)
2. Multi mapped read. (or)
3. Mate mapped to different 'Chr/scaffold/contig'

And may be others, but its good to look at the flag (column 2) and check whats happening.

http://broadinstitute.github.io/picard/explain-flags.html

ADD COMMENT • link modified 3.5 years ago • written 3.5 years ago by geek_y ♦ 8.5k

I am not sure If I understand you right but this is the histogram I am talking about

so Do i need to see all the sam file flags?

ADD REPLY • link modified 3.5 years ago • written 3.5 years ago by Medhat • 7.5k

<font size="2">What genome are you working with ? If the genome that you have used for reference mapping is not assembled into Chromosomes, with mate pair data, this may be possible, as the two pairs of a read mapped to different contigs/scaffolds as mate pair will have large inserts (3kb/5kb/10kb). Hence, it is normal to </font>have zero insert size <font size="2">for a mate pair data aligned to a draft genome.</font>

But, could you let me know whats the size of the mate pair fragment during library prep ?

ADD REPLY • link written 3.5 years ago by geek_y ♦ 8.5k

Library size is 8 kb . and this big zero column i could not explain it , so according to your answer shall I count it as pairs that mapped to different locus?! or you have other suggestion? could it be library preparation problem?

ADD REPLY • link written 3.5 years ago by Medhat • 7.5k

Which genome it is ? Is it assembled to Chromosome level ? If not, you can not comment on wetlab. Wet lab personnel may have checked the library size before sequencing with instrument such as BioAnalyzer. Check with them if they have insert size profile ?

ADD REPLY • link written 3.5 years ago by geek_y ♦ 8.5k

Maize genome and I mapped it against reference from genebank

ADD REPLY • link written 3.5 years ago by Medhat • 7.5k

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