hisat3_snakemake

A work in progress snakemake pipeline for running HISAT-3N

Also includes some downstream work to turn the transition table into bigwig files, as well a script to add on the extra BAM tags used by SlamDunk

Name		Name	Last commit message	Last commit date
Latest commit History 274 Commits
config		config
scripts		scripts
.gitattributes		.gitattributes
README.md		README.md
align.smk		align.smk
call_md.smk		call_md.smk
cluster_qsub.sh		cluster_qsub.sh
helpers.py		helpers.py
make_bigwigs.smk		make_bigwigs.smk
quickrule_hack_stability_run.smk		quickrule_hack_stability_run.smk
run_calculate_conversion_rate.smk		run_calculate_conversion_rate.smk
run_calculate_splice_stability.smk		run_calculate_splice_stability.smk
snp_mask.smk		snp_mask.smk
split_converted.smk		split_converted.smk
submit.sh		submit.sh
submit_2.sh		submit_2.sh
submit_calmd.sh		submit_calmd.sh
submit_mask.sh		submit_mask.sh
submit_quick_stab.sh		submit_quick_stab.sh

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