Snakemake pipelines for detecting RNA-editing from RNA-seq data.
A collaboration between the Raj lab and the Breen lab.
snakemake
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list of BAM files (must be aligned with MD flag)
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List of known SNPs to ignore
I have the latest version of dbSNP as a BED file here: /sc/hydra/projects/ad-omics/data/references//hg38_reference/dbSNP/dbSNP_GCF_000001405.38.bed
- human genome build
This is here:
/sc/hydra/projects/ad-omics/data/references//hg38_reference/hg38.fa
Measures global editing rates of Alu elements at all the possible editing types.
Has specific dependencies - to be covered.
Measures de novo editing genome-wide, applies some basic filters, annotates with gene and transcript consequences
This is a specific C to T RNA editing pipeline. Makes use of the Yeo lab SAILOR pipeline which they've exported as a singularity image. This pipeline just wraps that image inside snakemake so we can apply it on large datasets and summarise the results.
The C to T version of SAILOR has been given to the Raj lab by Brian Yee.