Can I get the SNPs from my RNA-Seq fastq files?

Hello,

I was asked if I can know/obtain the SNPs in the samples we sequenced with RNA-Seq. Can I do it from the .fastq files? How can I do it? Also, these fastq files mapped agains reference with 50M reads, would that be enough? Do I need to compute coverage?

Thank you

rna snp fastq rna-seq

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updated 7.8 years ago by S AR

• written 7.8 years ago by Pin.Bioinf

Hello Pin.Bioinf!

Please use the search function. It has been discussed multiple times before. This post may serve as a starting point from where you can dig further.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

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written 7.8 years ago by ATpoint

Also take a look here: A: Inferring genotype based on RNA sequnces

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written 7.8 years ago by Kevin Blighe

1 answer

Yes it is possible the same way as of whole genome. And its enough if it align a little bit it will give you snps on position of alignment. You can check :

Variant calling blog

2018 publication on Variant calling from RNA-seq data

Gatk variant calling pipeline on RNA seq data

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written 7.8 years ago by S AR

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