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capricy 03-11-2017 06:27 AM

library insert size: too small

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 06:42 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 08:44 PM

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

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