Question: SNP calling in de novo transcriptomics
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gravatar for deepak.fbt-pa4-02
2.4 years ago by
deepak.fbt-pa4-020 wrote:

I am Deepak, working on transcriptomics of asian cat fish. I have done de novo assembly of reads obtained through illumina sequencing. I have done SNP calling through VDAP-GUI usig the assembled contigs as the reference and i got almost 1,39,812 SNPs. Because refernce genome of asian cat fish is not yet available in public domain, so could i annotate these SNP? if yes then how? Please help me!!!!!!!

snp rna-seq next-gen assembly • 1.1k views
ADD COMMENTlink written 2.4 years ago by deepak.fbt-pa4-020

First you have to call genes on the contigs using Glimmer, or similar. Then they need to be functionally annotated. Until you have functionally annotated gene calls on your contigs, SNP-calling and annotation are not very useful, other than for comparing population diversity, or something similar. What are you planning on using the variant calls for?

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by Brian Bushnell16k
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