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