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TOBIAS_snakemake/example_config.yaml
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| #-------------------------------------------------------------------------# | |
| #-------------------------- TOBIAS input data ----------------------------# | |
| #-------------------------------------------------------------------------# | |
| data: | |
| Bcell: [data/Bcell_chr4.bam] #list of .bam-files | |
| Tcell: [data/Tcell_chr4_*.bam] #list of .bam-files | |
| run_info: | |
| organism: human #mouse/human | |
| fasta: data/genome_chr4.fa.gz #.fasta-file containing organism genome | |
| blacklist: data/blacklist_chr4.bed #.bed-file containing blacklisted regions | |
| gtf: data/genes_chr4.gtf #.gtf-file for annotation of peaks | |
| motifs: data/individual_motifs/* #motifs (directory with files or individual files in MEME/JASPAR/PFM format) | |
| output: test_output #output directory | |
| #-------------------------------------------------------------------------# | |
| #----------------------- Default module parameters -----------------------# | |
| #-------------------------------------------------------------------------# | |
| macs: "--nomodel --shift -100 --extsize 200 --broad" | |
| atacorrect: "" | |
| footprinting: "" | |
| bindetect: "" |