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
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written
by
Deepblue •
2 answers
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:
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
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