| name: run_fimo |
| task_type: fimo |
|
|
| debug: true |
|
|
| paths: |
| input_csv: dpacman/data_files/processed/fimo/remap2022_crm_fimo_input.csv |
| json_dir: dpacman/data_files/raw/genomes/hg38 |
| input_fasta_outer_dir: dpacman/data_files/processed/fimo/chrom_inputs |
| fimo_outdir: dpacman/data_files/processed/fimo/fimo_out |
| seq_fasta: to_scan.fa |
| bg_model: bg_model.txt |
|
|
| meme: |
| fimo_bin: /vast/projects/pranam/lab/shared/meme/bin/fimo |
| fasta_get_markov: /vast/projects/pranam/lab/shared/meme/libexec/meme-5.5.8/fasta-get-markov |
| jaspar_motif_file: /vast/projects/pranam/lab/shared/meme-5.5.8/tests/common/JASPAR_CORE_2014_vertebrates.meme |
|
|
| fimo: |
| thresh: 1e-2 |
| thresh_mode: q |
| max_stored: 1000000 |
| njobs: 64 |
|
|
| chroms: [1] |
| all_caps: true |
|
|
