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conf.txt.template
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conf.txt.template
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### Modify the paths etc accordingly.
### Case sensitive for all section names, parameters, and values
## Add a genome section to reflect the genome of interest.
## If there are multiple genomes, each genome must have its own section.
## When amplicon sequence is used as reference, this section is ignored.
#
[hg38]
ref_fasta = /bfx/genome/hg38/hg38.fa
bwa_idx = /bfx/genome/hg38/hg38.fa
refGene = /bfx/genome/hg38/hg38_UCSCrefGene.txt
[hg19]
ref_fasta = /bfx/genome/hg19/hg19.fa
bwa_idx = /bfx/genome/hg19/hg19.fa
refGene = /bfx/genome/hg19/UCSCrefGene.txt
[mm10]
ref_fasta = /bfx/genome/mm10/mm10.fa
bwa_idx = /bfx/genome/mm10/mm10.fa
refGene = /bfx/genome/mm10/mm10_UCSCrefGene.txt
[rn6]
ref_fasta = /bfx/genome/rn6/rn6.fa
bwa_idx = /bfx/genome/rn6/rn6.fa
refGene = /bfx/genome/rn6/rn6_UCSCrefGene.txt
[canFam3]
ref_fasta = /bfx/genome/canFam3/canFam3.fa
bwa_idx = /bfx/genome/canFam3/canFam3.fa
refGene = /bfx/genome/canFam3/canFam3_UCSCrefGene.txt
[criGri1]
ref_fasta = /bfx/genome/criGri1/criGri1.fa
bwa_idx = /bfx/genome/criGri1/criGri1.fa
refGene = /bfx/genome/criGri1/criGri1_UCSCrefGene.txt
[genomex]
ref_fasta = genome/genomex.fa
bwa_idx = genome/genomex.fa
refGene = genome/refgenex.txt
## Required tools
[app]
# The paths of prinseq and abra must be provided.
# For others, if path is not provided, it must be accessible
# in your environment
abra = /bfx/app/bin/abra-0.97-SNAPSHOT-jar-with-dependencies.jar
# Path to prinseq-lite.pl. Make sure prinseq path is executable.
prinseq = /bfx/app/bin/prinseq-lite.pl
# bwa (e.g. 0.7.15) must support bwa mem -M, and be searchable in environment variable PATH
# samtools
samtools = /bfx/app/bin/samtools
# Path of flash. By default use flash in PATH.
flash = /bfx/app/bin/flash2
# bedtools (e.g. v2.25) must support: bedtools intersect -F
bedtools = /bfx/app/bin/bedtools
# java must be 1.7 or later
java = /usr/bin/java
# pysamstats
pysamstats = /bfx/app/bin/pysamstats
# R must have ggplot2, reshape2, and naturalsort packages
rscript = /bfx/app/bin/Rscript
## Filtering parameters
[prinseq]
# remove reads with quality score mean below this value (default: 30)
min_qual_mean = 30
# remove reads with length less than this value (default: 50)
min_len = 50
# remove reads with percentage of Ns over this value (default: 3).
ns_max_p = 3
[other]
# realign for large indel detection with ABRA: Y(default) or N
realign_flag = Y
# require minimum BWA mapping quality score (default: 20)
min_mapq = 20
# number of bases on each side of sgRNA to view base changes (default: 40)
wing_length = 100
# Whether to use very high resolution in plots.
# Default: 0. This creates PNG images of 72 ppi resolution. Good for web viewing.
# If set to 1, TIFF images of 1200 ppi will be created and may be good for publication.
# TIFF images may not be viewable in major web browsers, but can be opened
# using common graphics software.
high_res = 0
# To control how many cores are needed to process one sample in SGE cluster
# The list of parallel environments can be found by 'qconf -spl'
parallel_env = orte
cores_per_job = 12