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Old 03-11-2017, 05:27 AM   #1
capricy
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Default 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!
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Old 03-11-2017, 05:42 AM   #2
GenoMax
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What kind of an experiment is this? It may still be fine to use that data after appropriate trimming. You could optionally merge.
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Old 03-11-2017, 07:44 PM   #3
capricy
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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.
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