nadjano/alevin-fry_test

snRNA-mapping-rate: Pipeline to compare mapping rates accross different tools for single-nuclei RNA sequencing experiments.

Runs Alevin, Alevin-fry, kb-tools and STARsolo on snRNA-Seq data with intron containing and intron free references.

Requirements

Nextflow (version 21.10.6)

How to run

nextflow run 'https://github.c/ebi-gene-expression-group/snRNA-mapping-rate.git' -r main \
--sdrf [srdf.txt] \
--resultsRoot [resultsDir] \
--referenceGenome [DNA.fa] \
--referencecDNA [cDNA.fa.gz] --referenceGtf [File.gtf] \
-config (change sequencing type to uppercase (10xv2 --> 10XV2))

Output

	MR1	MR2	MR3
Alevin
Alevin-fry
kb-tools
STARsolo

MR1: Mapping rate with standard single-cell options
MR2: Mapping rate with custom gtf file where 'trancript' is replaced with 'exon'
MR3: Mapping rate with single-nucleus options