Question: SNP calling,consensus sequence and running Blastn
gravatar for low.weiquan
4.8 years ago by
low.weiquan0 wrote:

Dear esteemed professionals,

After running a simple snp calling pipeline bwa -> mpileup(SAMtools) -> seqtk I have obtained a fasta file that has a single nucleotide sequence as a consensus sequence (for virus). However I noticed that some nucleotides are ambiguous like M and Y for example that can represent multiple nucleotides. So I ran Blastn using a database from my directory which is a fasta file with multiple virus nucleotide sequences that contain no ambiguous nucleotides. However when I open the output file the E-value for all sequences are 0. Is there anyway to replace the ambiguous sequences with highest occuring nucleotide during the snp calling pipeline or an option that I can use for Blastx package that allows proper handling of ambiguous nucleotides. 

Thank you all so much for helping, any advice is greatly appreciated.

The blast process is(on unix):

makeblastdb -in db.fa -dbtype nucl

blastn -query cnc.fa -db db.fa -out result.fa

snp blast • 1.7k views
ADD COMMENTlink modified 4.8 years ago • written 4.8 years ago by low.weiquan0
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