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config.yml
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# Container options -----------------------------------------------------------
# option to use Singularity for running the pipeline via containerized environments (True or False)
USE_SINGULARITY: True
# path to folder containing Singularity container image files (.sif files) for pipeline
SINGULARITY_IMAGE_FOLDER: "/home/groups/MaxsonLab/software/singularity-containers/pipeline_containers/cuttag/image_files"
# Quality Control -------------------------------------------------------------
FASTQ_SCREEN: src/fastq_screen.conf
# Adapter Trimming ------------------------------------------------------------
# option to trim adapters from raw reads to improve alignment rate (True or False)
TRIM_ADAPTERS: True
# FASTA file containing additional list of sequences to trim from reads
# ignored if TRIM_ADAPTERS is False
ADAPTER_FASTA: src/adapter_seqs.fa
# Alignment + preprocessing -------------------------------------------------------------------
GENOME: /home/groups/MaxsonLab/indices/GRch38/bowtie2/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.bowtie_index
# /home/groups/MaxsonLab/indices/GRch38/bowtie2/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.bowtie_index
# /home/groups/MaxsonLab/indices/mm10/bowtie2/mm10
FASTA: /home/groups/MaxsonLab/indices/homer_preparsed/GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta
#-----If running Homer (pipeline default), use one of the following homer_preparsed FASTA symlinks:
# /home/groups/MaxsonLab/indices/homer_preparsed/GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta
# /home/groups/MaxsonLab/indices/homer_preparsed/mm10.fa
#-----If not running Homer, use one of the following FASTA files:
# /home/groups/MaxsonLab/indices/GRch38/bowtie2/GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta
# /home/groups/MaxsonLab/indices/mm10/bowtie2/mm10.fa
GENES: genes/hg38_refseq_genes.bed
# genes/mm10_refseq_genes.bed
# genes/hg38_refseq_genes.bed
# Peak Calling ----------------------------------------------------------------
#should we use IGG for peak calling or not? (True or False)
USEIGG: True
# how is IgG spelled in the filename, eg: "IgG" for file "G1_IgG_Kasumi_S25_R2.fastq.gz"
IGG: IgG
CSIZES: src/hg38.chrom.sizes
# src/mm10.chrom.sizes
# src/hg38.chrom.sizes
# Peak Processing
N_INTERSECTS: 2 # the number of times a peak must appear across biological replicates (within one condition) to be considered a consensus peak
# (optional) path to tab-delimited file of blacklisted genomic regions to filter out
# if you don't want to remove regions, set this to "" (include quotations)
BLACKLIST: ""
# ----- CUT&RUN-specific blacklists from Nordin, A., Zambanini, G., Pagella, P. et al. 2023:
# blacklists/hg38_cutrun_blacklist_Nordin2023.txt
# blacklists/mm10_cutrun_blacklist_Nordin2023.txt
# ----- ENCODE blacklists from Amemiya, H.M., Kundaje, A. & Boyle, A.P 2019:
# blacklists/ENCODE_hg38-blacklist.v2.bed
# blacklists/ENCODE_mm10-blacklist.v2.bed
# Diffbind settings ----------------------------------------------------------------
# filter for Diffbind differential analyis results with pval less than <padj_cutoff>
padj_cutoff: 0.05