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config.yaml
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config.yaml
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########################################################
# this is the config file of snakemake for chip-seq analysis, use it before, your should install software: trimmomatic, bowtie2, samtools, bamtools, GEM,
# write by zhanweimin, [email protected]
# 2019.3.13
# I will update it after a half year
########################################################
#the trimmomatic software, it's to filter fastq file
Trimmomatic: /home/zhan/biosoft/trimmomatic/Trimmomatic-0.38/trimmomatic-0.38.jar
#trimmomatic sofware's adapt fasta
Truseq_fa: /home/zhan/biosoft/trimmomatic/Trimmomatic-0.38/adapters/TruSeq2-SE.fa
#the GEM software, it's to find peak
Gem: /home/zhan/biosoft/gem/gem
#reference indival chromosome directory
Reference_dir: /disks/reference/sequence/indival_fa
#reference genome
reference: /disks/reference/sequence/genome_fa/Zea_mays.B73_RefGen_v4.dna.chromosome.fa
#this file content the length's of genome chromosome
Chrom_size: /disks/reference/annotation/chrom.sizes
#this is the genome index, that is uesd for the bowtie2 alignment
Index: /disks/reference/index/bowtie2_index/Zea_mays.B73_RefGen_v4.dna_index
#that is the genome's annotation, must the gtf format
Gtf_dir: /disks/reference/annotation/Zea_mays.AGPv4.37.gtf
#
genome_sqlit: /disks/reference/annotation/maize_v4_2018_11.sqlite
#the samples fastq file prefix, it must is "Y_2.cleaned_2.fastq.gz" format, "Y" is the sample's name, "2" is the replace's times
samples: ["AG"]
#the contrals file prefix, it must is "HALO_2.cleaned_2.fastq.gz" format, "HALO" is the contral's name, "2" is the replace
contrals: ["HALO"]
#the replace times
reps: ["1","2"]