Get a specific genotype information of RNASeq fastq files

Question

[shangyuan5000]

Hi, I have the RNA-seq data at hand, and want to get the genotype information at a specific gene location. Is there any easy way to do this?

regard, Raymond

[Kevin Blighe]

Please read my answer here: A: Inferring genotype based on RNA sequnces

[shangyuan5000]

Thanks for the kind reply. Actually, what I want is quite simple: my interested gene has two different genotypes (and they are even different in protein sequences in some positions!), and I want the related genotypes from my RNASeq data. I think this question should be much easier than that when you want to determine all the genotypes everywhere, and it should have a good chance to address it as long as the RNAseq fasta files capture those coding regions that determine the genotypes.

I guess I may made two libraries from the two paired fastq files, and align the transcript of my target gene to it and check the genotypes mannually. Does this make sense? Even though it's a little bit time costing.

Thanks & Regards, Raymond

[Kevin Blighe]

So, you just need to split the reads into 2 separate files based on a genotype?

[shangyuan5000]

No. I made a blastdb from the fasta files(read length 101), and then blast the -100~+100 sequence of my allele site to the blastdb, and check all hits that include the allele site to see whether my interested allele appears or not.

Answer 1

[swbarnes2]

Eyeball the locus in IGV.

Answer 2

[shangyuan5000]

I tried the method by natasha.sernova: A: Finding specific gene in reads It works for my question.

[Kevin Blighe]

That's great to hear. Thanks for the feedback, Raymond.

[shangyuan5000]

My current solution is quite clumsy, with the blastn result, there are hundreds of hits with pvalue at range of E-30 or lower, and I checked them by search the NT nearby the SNP sites and confirmed the Allele information. Thanks for your kind reply, and for the review of SNP calls from RNASeq.