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Old 01-02-2018, 02:19 AM   #1
analyticalscientist
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Location: Bengalore

Join Date: Jan 2018
Posts: 1
Default How to analysis with allotetraploid genome

Hi
I recently got SNP analysis of allotetraploid genome(AADD genome type)
My steps are
Fastqc
trimming
next is mapping onto reference genome
My concern is with homoelogous region how should i tackle this whjile mapping?
Is there quality filtering parameter which can tackle homoelogous region and give true SNPs and Indels
Also what are concern should i put while doing QC and trimming?
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