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Old 08-07-2011, 12:19 PM   #1
athena.uci
Junior Member
 
Location: USA

Join Date: Mar 2011
Posts: 1
Default bwa insert size estimation

Hi everyone,

I ran bwa on some data, but i don't understand the insert size estimation part.

for Example, what I see is

inferred external izise ....: 183.980 +/- 18.194
.......
inferred maximum insert size : 312 (7.04) sigma


but I'm confused , because my read length is 100bp for each end, so if the mean of external isize is 183, it means to reads coincide!!

so I'm assuming something is wrong here. can someone please help me.

Thanks,
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Old 11-07-2011, 07:12 AM   #2
marcowanger
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Location: Hong Kong

Join Date: Dec 2008
Posts: 350
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Hi athena,

Latest illumina seq. can let the two end of read to overlap. i.e. sequencing the entire fragment with some overlap.

May you check with your sequencing spec?

Marco

Quote:
Originally Posted by athena.uci View Post
Hi everyone,

I ran bwa on some data, but i don't understand the insert size estimation part.

for Example, what I see is

inferred external izise ....: 183.980 +/- 18.194
.......
inferred maximum insert size : 312 (7.04) sigma


but I'm confused , because my read length is 100bp for each end, so if the mean of external isize is 183, it means to reads coincide!!

so I'm assuming something is wrong here. can someone please help me.

Thanks,
__________________
Marco

Last edited by marcowanger; 11-07-2011 at 07:14 AM.
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Old 11-07-2011, 09:49 AM   #3
swbarnes2
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Location: San Diego

Join Date: May 2008
Posts: 912
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Overlap isn't impossible. If that's what your data says is happening, then that's what's happening. You should talk to the people preparing the samples. Find out what insert size they are aiming for, and what insert size their instruments tell them they have, and then show them what the sam files say the average insert size really is. It might not be so smart for them to run 100 bp reads if their fragments are routinely that short. They should aim for larger fragments, or save time and money and not sequence 100 bp.
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