Question: making a custom reference
0
gravatar for shynilasanthi
2.5 years ago by
Sri Lanka
shynilasanthi30 wrote:

I have illumina short reads which I want to call SNP without using a reference genome. I want to make a consenses sequence of some selected reads and then align the other reads to it. so the basic idea is that the consensus sequence need to be act like a "dummy genome" Is there any way to do this?

snp alignment assembly genome • 635 views
ADD COMMENTlink modified 2.5 years ago by ori50 • written 2.5 years ago by shynilasanthi30
1
gravatar for toralmanvar
2.5 years ago by
toralmanvar840
toralmanvar840 wrote:

You can first denovo assemble the reads to generate consensus/contigs and then its can be used as reference to map back reads to it and call SNPs.

ADD COMMENTlink written 2.5 years ago by toralmanvar840
1
gravatar for ori
2.5 years ago by
ori50
ori50 wrote:

I think SNP is at the base position that the base in one genome (ex: genome A) is different from the base in the other genome (ex: genome B).
From your question, it seems that the reads derived from genome A and genome B are mixed in the data, and
genome A = sequences produced by some selected reads;
genome B = sequences produced by other reads.

I wonder how you extract reads of genome A from the original data, but if you can do that, I agree with toralmanvar.
You should assemble the reads derived from genome A, and you will get contigs that you called “dummy genome”.
Then you align the reads derived from genome B to the contigs of genome A, and you will detect SNPs.
I recommend that you also align the reads derived from genome A to the contigs of genome A at that time, to compare the allele frequency of two genomes.

ADD COMMENTlink written 2.5 years ago by ori50
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2005 users visited in the last hour