RNA パイプライン設定ファイルについて

RNA解析パイプライン実行時に読込まれるファイルです.各ツールのフィルタリングの閾値などのパラメータを設定することができます.

注釈

HGCスパコンの場合,このファイルは /home/w3varann/genomon_pipeline-2.4.1/genomon_conf/ にあります.

rna解析用:rna_genomon.cfg
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#
# Genomon pipeline configuration file
#

[REFERENCE]
# prepared reference fasta file
star_genome                             = # the path to the GRCh37.STAR-2.5.2a
ref_fasta                               = # the path to the reference genome

[SOFTWARE]
# prepared tools
samtools                                = # the path to the samtools-1.2/samtools
tophat2                                 = # the path to the tophat-2.0.14.Linux_x86_64/tophat2
STAR                                    = # the path to the STAR-2.5.2a/bin/Linux_x86_64/STAR
STAR-Fusion                             = # the path to the STAR-Fusion-master/STAR-Fusion
bedtools                                = # the path to the bedtools
biobambam                               = # the path to the biobambam-0.0.191/bin
blat                                    = # the path to the blat_x86_64/blat
htslib                                  = # the path to the htslib-1.3
fusionfusion                            = # the path to the bin/fusionfusion
fusion_utils                            = # the path to the bin/fusion_utils
chimera_utils                           = # the path to the bin/chimera_utils
intron_retention_utils                  = # the path to the bin/intron_retention_utils
genomon_expression                      = # the path to the bin/genomon_expression
genomon_pa                              = # the path to the bin/genomon_pa
pa_plot                                 = # the path to the bin/pa_plot

[ENV]
PERL5LIB                                = # the path to the perl module
PYTHONHOME                              = # the path to the python home
PYTHONPATH                              = # the path to the python path
LD_LIBRARY_PATH                         = # the path to the python library


######################################################################
#
# Analysis parameters
#
#   If not defined, default values are going to be used in the pipeline.
#

##########
# parameters for bam2fastq
[bam2fastq]
qsub_option = -l ljob,s_vmem=1G,mem_req=1G

##########
# parameters for star alignment
[star_align]
qsub_option = -pe def_slot 6 -l s_vmem=5.3G,mem_req=5.3G
star_params = --runThreadN 6 --outSAMstrandField intronMotif --outSAMunmapped Within --alignMatesGapMax 500000 --alignIntronMax 500000 --outSJfilterOverhangMin 12 12 12 12 --outSJfilterCoun    tUniqueMin 1 1 1 1 --outSJfilterCountTotalMin 1 1 1 1 --chimSegmentMin 12 --chimJunctionOverhangMin 12 --outSAMtype BAM Unsorted
samtools_sort_params = -@ 6 -m 3G

##########
# parameters for fusionfusion
[fusion_count_control]
qsub_option = -l ljob,s_vmem=5.3G,mem_req=5.3G
params =

[fusion_merge_control]
qsub_option = -l ljob,s_vmem=5.3G,mem_req=5.3G
params =

[fusionfusion]
qsub_option = -l ljob,s_vmem=5.3G,mem_req=5.3G
annotation_dir = # the path to the fusionfusion/resource
params=
filt_params = --filter_same_gene

[genomon_expression]
qsub_option = -l ljob,s_vmem=5.3G,mem_req=5.3G
annotation_file = # the path to the resource/exon.GRCh37.bed
params=

[intron_retention]
qsub_option = -l ljob,s_vmem=5.3G,mem_req=5.3G
ref_gene = # the path to the resource/refGene.txt.gz
params= --chr_name_list # the path to the resource/ucsc2grch.txt

##########
## Post Analysis
[pa_plot]
enable = True
include_unpair = True
include_unpanel = True
title = Genomon_RNA
remarks = Data used in this report were generated using below software.
software = genomon_pipeline:Genomon-Pipeline, STAR:STAR, fusionfusion:fusionfusion

config_file = # the path to the paplot-0.4.0/paplot.cfg
qsub_option = -l s_vmem=2G,mem_req=2G

[post_analysis]
enable = True
config_file = # the path to the GenomonPostAnalysis-1.2.0/genomon_post_analysis.cfg
qsub_option = -l s_vmem=2G,mem_req=2G