Kallisto_Snakemake

Originally forked from https://github.com/bhklab/Snakemake/tree/master/Kallisto_Snakemake

Snakemake pipeline for RNASeq analysis using Kallisto on Slurm

• Use Kallisto_Index pipeline to build the Kallisto Index using the latest GENCODE transcriptome.
• Use Run_Kallisto pipeline to run Kallisto on raw fastq files. If you have multiple samples.The pipeline will automatically submit news jobs into the cluster.

STEP 1: Login to cluster:

ssh username@cluster.org

STEP2: Download repo, genome references and example data

Download Kallisto transcriptome and create index

salloc -c 1 -t 2:00:00 --mem=6G -p build

git clone https://github.com/LupienLab/kallisto_snakemake.git

cd kallisto_snakemake/Kallisto_Index

snakemake --snakefile Snakemake --cores 1

STEP 3: Edit config.yaml, samples.tsv and provide correct paths:

cd kallisto_snakemake/Run_Kallisto

vi config.yaml 

vi samples.tsv

STEP 4: Run Kallisto with snakemake command on cluster:

sbatch sbatch.sh