Mate pair distance calculation
 

Hi

I have two mate pair libraries with 2-3 kb and 6-8 kb inserts from a plant species. The libraries have been sequenced 2x100 cycles. FastQC shows good quality reads with low duplication levels. I do not have a reference genome for the species. I wondering if there is an easy way to check the distance between paired reads to see how many of reads are from the expected fragments sizes.

No. It is not possible without a reference.
You could do an assembly to generate a reference. abyss-PE calculates the pair distances during assembly.

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Phillip

Thanks pmiguel. Is mapping to organnells genome is a good option. I know that their size is smaller in comparison to nuclear genome, but they are available for some close relatives of the species.

You could try that. Depending on how close your sample genome is to the one you are using as a reference you will get an answer. That may not necessarily be accurate but would at least give you a ball park idea of the insert size distribution.

Yes. Also, for plant samples you can usually assemble the chloroplast from just a fraction of the data because of the high molar contribution of chloroplast DNA to most plant genomic DNA preps.

But mapping to a relative would likely work as well. Doesn't matter if there areas that don't map, these areas have no reason to create bias in inter-pair distance measurements.

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Phillip