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.

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
#
# Genomon pipeline configuration file
#

[REFERENCE]
# prepared reference fasta file
star_genome                 = # the path to the GRCh37.STAR-STAR_2.4.0k

[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-STAR_2.4.0k/bin/Linux_x86_64/STAR
STAR-Fusion                 = # the path to the STAR-Fusion-master/STAR-Fusion
fusionfusion                = # the path to the bin/fusionfusion

[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 --outSJfilterCountUniqueMin 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
[fusionfusion]
qsub_option = -l ljob,s_vmem=5.3G,mem_req=5.3G
param_file = /home/w3varann/database/fusionfusion_hg19/param.cfg