Repository for running experiments with snakemake pipeline. Evaluation scripts for IsoCon.
Install snakemake (python3 only) link.
This experiment pipeline assumes you have IsoCon and ICE installed. You can however remove one of the tools as described in next section
You can remove tools or experiments by changing the fields in the config file simulated_experiments.json. To remove an experiment, change "EXPERIMENTS" : ["MEMBER_EXPERIMENT", "ISOFORM_EXPERIMENT", "COMBINED_EXPERIEMENT" ],, similarly, you can alter these fields to reduce the number or size of the experiments:
"GENE_MEMBERS" : ["HSFY2", "DAZ2", "TSPY13P"],
"READ_COUNTS" : [ "20", "100", "500", "2500", "12500"],
"RUNS" : ["1", "2", "3", "4", "5", "6", "7", "8", "9", "10"],
"ABUNDANCE" : ["constant", "exponential"],
"TOOLS" : ["ISOCON", "ICE"],
Modify all paths in simulated_experiments.json, then try a dry run as
snakemake --configfile simulated_experiments.json --latency-wait 100 --verbose -n
To start the actual pipeline, run the above command without parameter -n. This pipeline should be run on a cluster, below is a command to distribute jobs.
snakemake --keep-going -j 999999 --cluster "sbatch --exclude={cluster.exclude} -c {cluster.ntasks} -N {cluster.Nodes} -t {cluster.runtime} -J {cluster.jobname} --mail-type={cluster.mail_type} --mail-user={cluster.mail}" --cluster-config cluster.json --configfile simulated_experiments.json --latency-wait 100 --verbose -n
The experiment pipeline assumes you have the software ToFU, ccs, and bax2bam installed to preprocess the Iso-Seq data (these three are all included in pacbio SMRTLink suite). IsoCon, ICE, and proovread will be needed to run downstream processing of CCS reads but any of these softwar can be removed from the pipeline (therefore does not have to be installed) by mdifying the TOOLS field in the config file experimental_experiments.json .
"TOOLS" :["ISOCON", "ICE_QUAL", "PROOVREAD"]