Question: Aligning transcript with known position for SNP to draft genome to find the position of SNPs
0
gravatar for dasakan
6 months ago by
dasakan0
dasakan0 wrote:

Hi, I have assembled transcriptome (sequenced by RNAseq) with known position of SNPs (Vcf file is there). In the mean time, I have received the draft genome in different scaffolods. To design probe to amplify the SNP target, I am interested to use the genome sequences, however, I donot know the SNP locus in genome. Is there any tool, to align the transcripts in the draft genome and extract the corresponding SNP position within the scaffold sequences keeping the info of respective transcript ids too? It may be like BED coordinates of transcripts in the draft genome.

snp alignment genome • 223 views
ADD COMMENTlink modified 6 months ago by Vitis2.2k • written 6 months ago by dasakan0
0
gravatar for Vitis
6 months ago by
Vitis2.2k
New York
Vitis2.2k wrote:

Both BLAST and BLAT may be able to do it. I'd try BLAT first. Then it would be straightforward to parse the BLAT result to match the variant positions.

https://metacpan.org/pod/Bio::Tools::Blat

ADD COMMENTlink written 6 months ago by Vitis2.2k

Thanks:) will try that way..

ADD REPLYlink written 6 months ago by dasakan0
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