Recombination events from single end reads.

Question

[Adrian Pelin]

Hello,

I have 5 strains mixed in culture and propagated and I am trying to measure recombination rates by sequencing total DNA extracted after certain periods of time. My sequencing is single end reads, from 150bp to 300bp.

I have the genomes of the 5 strains that are mixed, and know the locations of SNPs. Is there any software that I can use to find SNPs specific to 2 different strains within one reads, which might indicate that the read comes from a recombinant species.

Adrian

Answer 1

[Pierre Lindenbaum]

I would use my tool https://github.com/lindenb/jvarkit/wiki/SAM2Tsv to:

get the name of the reads having a mutation at position N1 for REF1 | sort> list1

get the name of the reads having a mutation at position N2 for REF2 | sort> list2

comm list1 list2 > result

[Adrian Pelin]

This seems like a solid approach. Would I have to map to one reference only in this case, or to all 5 at the same time? I was planning to map to all 5 strains simultaneously, and then find reads that mapped to ref1 but have mutation at position N1 for REF2?

[Pierre Lindenbaum]

Hard to answer without knowing how close are your 5 references. I would use one reference only per strain. (= 5 BAMs for 5 REFs) , using the same reads of course