CLAM_m6A_Snakemake

Snakemake pipeline of CLAM processing m6A RIP-seq (MeRIP)

Instructions

1.a Running from download of SRA:

Configure the "config.yaml" file by running "configure.py"

python configure.py GSE12345

1.b Running from local reads/fastq files

Alternatively, just make a "{project}/{reads}" directory, and put the corresponding files in

python make_ln.py

source activate py36
PROJECT={project} snakemake -n

To accomadate the changed GEO API (the code actually updated back on March 2018), use the following command to prepare a GEO run:

python2 scripts/geo_downloader/getSRApath.py GSE52600 projects/GSE52600/config/sra_dir.txt

Once the sra_dir.txt file is prepared, run

python2 configure.py GSE52600

Then submit it by

./prepare_individual_run.sh GSE52600

Name		Name	Last commit message	Last commit date
Latest commit History 30 Commits
contrib		contrib
scripts		scripts
.gitignore		.gitignore
GenReport_Snakefile		GenReport_Snakefile
LICENSE		LICENSE
README.md		README.md
Snakefile		Snakefile
Snakefile_bak20180330		Snakefile_bak20180330
clusterconfig.yaml		clusterconfig.yaml
config.template.yaml		config.template.yaml
config.yaml		config.yaml
configure.py		configure.py
make_ln.py		make_ln.py
make_ln_2.py		make_ln_2.py
parse_peaks.py		parse_peaks.py
prepare_individual_run.sh		prepare_individual_run.sh
re_touch.sh		re_touch.sh
run_snakemake.sh		run_snakemake.sh
submit.sh		submit.sh