Hi, folks:
I am doing research on Arabidopsis. The existing reference genome is on one ecotype (Col), and we have sequenced another ecotype (Ws), since we have mutants based on Ws.
What should I do if I want to use Ws as a reference genome?
I have used bowtie to align the Ws reads to Col and use Samtools/GATK try to find any indels/SNPs, however, my target is to be able to get a new reference genome based on Ws, what should I do?
Any suggestions are much appreciated.
Thx.
I am doing research on Arabidopsis. The existing reference genome is on one ecotype (Col), and we have sequenced another ecotype (Ws), since we have mutants based on Ws.
What should I do if I want to use Ws as a reference genome?
I have used bowtie to align the Ws reads to Col and use Samtools/GATK try to find any indels/SNPs, however, my target is to be able to get a new reference genome based on Ws, what should I do?
Any suggestions are much appreciated.
Thx.
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