Question: Qualimap insert size result explanation
0
gravatar for Medhat
3.5 years ago by
Medhat7.5k
Poland
Medhat7.5k wrote:

for  Qualimap users

what is the meaning of zero insert in the insert size histogram?

knowing that mapping was mate pairs 

does it means that one sequence was aligned and the other not ? or the aligned in different locus? 

 

 

sequencing blast alignment • 1.4k views
ADD COMMENTlink modified 3.5 years ago by geek_y8.5k • written 3.5 years ago by Medhat7.5k
0
gravatar for geek_y
3.5 years ago by
geek_y8.5k
geek_y8.5k 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 COMMENTlink modified 3.5 years ago • written 3.5 years ago by geek_y8.5k

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 REPLYlink modified 3.5 years ago • written 3.5 years ago by Medhat7.5k

<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 REPLYlink written 3.5 years ago by geek_y8.5k

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 REPLYlink written 3.5 years ago by Medhat7.5k

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 REPLYlink written 3.5 years ago by geek_y8.5k

Maize genome and I mapped it against reference from genebank 

ADD REPLYlink written 3.5 years ago by Medhat7.5k
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