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TOBIAS/snakemake_pipeline/TOBIAS_example.config

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#-------------------------------------------------------------------------#
#-------------------------- TOBIAS input data ----------------------------#
#-------------------------------------------------------------------------#
data:
Tcell: [../test_data/day1_chr4.bam,../test_data/day2_chr4.bam,../test_data/day3_chr4.bam]
Bcell: [../test_data/buenrostro_chr4.bam]
run_info:
organism: human
fasta: ../test_data/homo_sapiens.94.chr4.fa
blacklist: ../test_data/homo_sapiens.blacklisted.chr4.bed
gtf: ../test_data/homo_sapiens.94.chr4.gtf
motifs: jaspar_core_vertebrates # adjust path
output: ../test_data/tobias_output
#-------------------------------------------------------------------------#
#----------------------- Default module parameters -----------------------#
#-------------------------------------------------------------------------#
macs: "--nomodel --shift -100 --extsize 200 --broad"
# for parameter description see uropa manual: http://uropa-manual.readthedocs.io/config.html
# adjust filter attribute for given gtf: ensembl gene_biotype / genecode gene_type
# other optional parameters: --filter_attribute gene_biotype --attribute_value protein_coding
uropa: "--feature gene --feature_anchor start --distance [10000,1000] --filter_attribute gene_biotype --attribute_value protein_coding --show_attribute gene_name,gene_id,gene_biotype"
atacorrect: ""
footprinting: ""
bindetect: ""
plotting: ""