SNP for RNA-Seq

Question

[Chan]

Hi all.I am currently working on SNP for RNA-Seq data and was wondering if I can use the samtools mpileup command for it ?

Thanks

[WouterDeCoster]

I would advise you to follow the GATK best practices for variant calling in RNA-seq

[Ram]

You mean to ask if you can use the samtools mpileup utility, surely? The command can be used anywhere you want :)

What kind of RNAseq data do you have? What organism is it for, and are you aligning it to a reference or assembling it de novo?

[Chan]

Thanks for the reply Ram.

Yes, I am not sure if I can use mplieup for RNA-Seq.

I am working on mouse model, Illumina HiSeq 2500, STAR aligner and reference based alignment.

[Ram]

I am working on mouse model, Illumina HiSeq 2500, STAR aligner and reference based alignment.

Please edit your question and add the above information to it. That way, people need not read through comments to get all relevant information.