example data

snakemake_pipeline/TOBIAS_example.config

@@ -0,0 +1,34 @@
+#-------------------------------------------------------------------------#
+#-------------------------- 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: /mnt/agnerds/annika.fust/motifs/jaspar_core
+  output: 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: ""