This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Genotyping tool for fasta sequences

Hello guys,there some tool I can genotyping my HRSV sequences in fasta format,in a fast way?

thanks in advance!!!

genome rna-seq genotyping
• 1,975 views • link
updated by Ram Ram • written by uirajan-kuki • uirajan-kuki

Could you please provide more info on this, using abbreviation might not help as many people might not be aware of them!

• 0 views • link
written by Sej Modha Sej Modha

HRSV = Human respiratory syncytial virus, in all likelihood.

uirajan-kuki : Why did you select rnaseq tag for your post? Is this RNAseq data? This is an RNA virus, so it must have been converted to DNA before sequencing (akin to RNAseq).

• 0 views • link
written by GenoMax GenoMax

YES,my sequnces are converted already,now I need to genotyping them...

• 0 views • link
written by uirajan-kuki • uirajan-kuki

Then align them to the reference genome sequence and then call variants. Have the reads been converted to fasta format for some reason? Do you have the original fastq reads available? If so use fastq version when you do the alignments.

• 0 views • link
written by GenoMax GenoMax

Congrats, if you have the dna/rna sequence of a virus in fasta format you have already genotyped it (somehow), because that is the genotype by definition. I am quite sure you meant something else, but you need to explain that better.

• 0 views • link
written by Michael Dondrup Michael Dondrup

0 answers

No answers yet.

Log in to answer this question.

More posts like this