ENCORE2_RNAseq

Commands

snakemake \
-s /tscc/projects/ps-yeolab3/bay001/codebase/ENCORE2_RNAseq/main.smk \
-j 30 \
--configfile inputs/ENCODE.yaml \
--cluster "sbatch -t {params.run_time} -e {params.error_file} -o stdout/{rule}.txt -p condo -q condo -A csd792 --tasks-per-node {threads} --mem {params.memory} --job-name {rule} --exclude tscc-11-[44,47-59,61-68,70-75,77]" \
--use-singularity \
--singularity-prefix /tscc/lustre/ddn/scratch/$USER/.singularity \
--singularity-args "--bind /tscc" \
--rerun-incomplete \
-p \
--notemp \
-w 120 \
--retries 3 \
--cluster-cancel scancel \
-n

How to make references

config["LABRAT_TXFASTA"]

    LABRAT.py --mode makeTFfasta \
        --gff {config.GFF} \
        --genomefasta {params.genome} \
        --lasttwoexons \
        --librarytype {params.libtype}

Caveats:

• SplISER is a huge time sink. Comment out if you want this to run a ton of jobs.
• Kind of a silly one, but do not include ".Aligned.sortedByCoord.out.bam" in either "ctrl_experiment" or "experiment" columns. This prefix is automatically appended during alignment, and I use string substitution to remove them for certain rules.
• For Yeolab: add --exclude tscc-11-[44,47-59,61-68,70-75,77]