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config.yaml
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config.yaml
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# Configuration file for ATAC-Seq
# quality control, alignment, macs ----------------------------------------------------------
# sequencing adapters to trim in fasta format.
ADAPTERS: "/home/groups/MaxsonLab/callahro/adapters/nextera_adapters.fasta"
# fasta file of genome for alignment.
REFERENCE: "/home/groups/MaxsonLab/indices/GRch38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta"
# fastq_screen config file
FASTQ_SCREEN_CONF: "config/fastq_screen.conf"
# effective size of the genome to be used for MACS peak calling
# genome_size: "1.87e9" #mouse default size
genome_size: "2.7e9" #human default genome size
# consensus peaks catalogue ------------------------------------------------------------------
#The metadata file that has a mapping from sample name to condition. Columns must be 'SampleID' and 'Condition'.
metadata_file: "config/metadata.tsv"
# select peaks that are in this many replicates per condition:
n_intersects: 2
#The location of the blacklist file that we will use to filter out regions that overlap a blacklist
# blacklist_file: "/home/groups/MaxsonLab/indices/mm10/mm10.blacklist.v2.bed"
blacklist_file: "/home/groups/MaxsonLab/indices/GRch38/hg38.blacklist.v2.bed"
#the name of the genome that you are using for usage
# genome_name: "mm10"
genome_name: "hg38"
# chip screen --------------------------------------------------------------------------------
chrom_sizes: "/home/groups/MaxsonLab/indices/GRch38/hg38.sorted.chrom.sizes"
# differential peaks -------------------------------------------------------------------------
significance: 0.05
# essential report ---------------------------------------------------------------------------
gen_report: yes # [yes, no]
title: "GSK x Quiz treatment with MOLM13 cells at 24 hours"
authors:
- Dan Coleman
- Rowan Callahan
- Garth Kong
- Ted Braun
- Julia Maxson
- et al.
intro: "We are looking to do some drug combination studies with GSK and Quizartinib to treat MOLM13 cells which have FLT3-ITD mutations."
analysis:
- "Trim reads via trimmomatic and align to genome using bowtie2."
- "Remove mitochondrial reads, remove PCR duplicate reads, shift reads, and make tracks."
- "Call peaks, take consensus peaks, and make the counts table."
- "Differential analysis via DESeq2 with Condition as variable."
takeaways:
- "takeaway 1"
- "takeaway 2"
- "takeaway 3"
notes: "We answered these questions, and look forward to answering more."