Question: SNP for RNA-Seq
0
gravatar for PC
2.1 years ago by
PC20
PC20 wrote:

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

rna-seq snp • 756 views
ADD COMMENTlink written 2.1 years ago by PC20
1

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

ADD REPLYlink written 2.1 years ago by WouterDeCoster39k

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?

ADD REPLYlink written 2.1 years ago by RamRS21k

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.

ADD REPLYlink written 2.1 years ago by PC20

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.

ADD REPLYlink written 2.1 years ago by RamRS21k
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