Finding mutations by Ilumina rna-seq data

Question

[Deepblue]

Hi,

I have rna-seq data that comes from a pool of evolved and reference bacterial strains. I would like to know if there has been any mutations in the genes in mutated strains, but can't afford genomics to find them. Is there any way/package to find mutations using my rna-seq data? They're all 2 × 150 bp.

Thank you

[cpad0112]

RNAseq data is not tested for variant calling vigorously. You can try the tutorial here: https://ssvbio.github.io/rna-seq-and-gatk-best-practices. In tutorial, tophat is used as tutorial is old. You can use hisat2 instead of tophat and probably you can skip step 9.

Answer 1

[kashiff007]

Although RNA-seq is not the desired data to call mutation (SNPs), since u are lacking with other genomics data use this pipeline from gatk:

Answer 2

[colindaven]

It's not ideal, but I would use samtools markdup to remove the duplicate reads, then use freebayes or samtools, or maybe snippy (more bacteria specific, but maybe just for WGS data).

There's a Galaxy tutorial here for general concepts: https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/microbial-variants/tutorial.html