library insert size: too small

capricy · 03-11-2017, 05:27 AM

Hello,

I got some illumina data which obviously has very small insert size as many of the read pairs have >95% overlap. I went back to illumina library protocol and feel that it generally suggests a library insert size longer than the total length of the paired-end read, that is, read pair does not overlap.

What is the optimal library insert size? Should I move forward for data analysis?

Thanks a lot!

GenoMax · 03-11-2017, 05:42 AM

What kind of an experiment is this? It may still be fine to use that data after appropriate trimming. You could optionally merge.

capricy · 03-11-2017, 07:44 PM

It is metagenomic data from fecal samples. I did trim the samples with trimmomatic.

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03-11-2017, 05:27 AM	#1
capricy Senior Member Location: 63130 Join Date: Apr 2012 Posts: 116	library insert size: too small Hello, I got some illumina data which obviously has very small insert size as many of the read pairs have >95% overlap. I went back to illumina library protocol and feel that it generally suggests a library insert size longer than the total length of the paired-end read, that is, read pair does not overlap. What is the optimal library insert size? Should I move forward for data analysis? Thanks a lot!

03-11-2017, 07:44 PM	#3
capricy Senior Member Location: 63130 Join Date: Apr 2012 Posts: 116	It is metagenomic data from fecal samples. I did trim the samples with trimmomatic. Last edited by capricy; 03-11-2017 at 07:46 PM.

03-11-2017, 05:42 AM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 6,385	What kind of an experiment is this? It may still be fine to use that data after appropriate trimming. You could optionally merge.