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List of Pipeline Parameters
Please check that the following parameters are correct before running the pipeline.
02_Review_Pipeline_Parameters.sh script run date:
Wed Jul 19 16:06:45 EDT 2017
Pipeline version:
v2.1.6
Refer to Pipeline_Version_History.txt for details.
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#--------------------------------------------------------------
"Global Variables"  = variables used by multiple steps
#--------------------------------------------------------------
Dataset_DIR=
/projectnb/wax-es/aramp10/G110_Samples
BU_User=
aramp10
VM_DIR_FASTQC=
/net/waxman-server/mnt/data/waxmanlabvm_home/waxmanlab/FASTQC/G110
#--------------------------------------------------------------
Check if VM_DIR_FASTQC exists:
Need to create VM_DIR_FASTQC!
Just created the remote directory.
#--------------------------------------------------------------
Dataset_Label=
G110
GTF_Files_DIR=
/unprotected/projects/waxmanlab/routines/GTF_Files
#--------------------------------------------------------------
"Step-specific Variables"  = variables used by a particular step
#--------------------------------------------------------------
#---------------------------
Job: TopHat_Single_End
Bowtie2Index_DIR=
/projectnb/wax-es/aramp10/Bowtie2
STRANDEDNESS=
fr-firststrand
#---------------------------
Job: CollectRnaSeqMetrics
STRAND_SPECIFICITY=
SECOND_READ_TRANSCRIPTION_STRAND
#---------------------------
Job: Extract_Counts
MODE=
intersection-nonempty
STRANDEDNESS_HTSeq=
reverse
STRANDEDNESS_featureCount=
2
#---------------------------
Job: bamCorrelate
zMin=
0.6
zMax
1.0
#---------------------------
Job: UCSC_BigWig
STRAND_RULE
+-,-+
#---------------------------
#--------------------------------------------------------------
"Additional Variables" = variables not user-specified
#--------------------------------------------------------------
#---------------------------
Job: Extract_Counts
FEATURE_ID
gene_id
#---------------------------
Sample_Labels_DIR
/projectnb/wax-es/aramp10/G110_Samples/Scripts/00_Setup_Pipeline
#---------------------------
SCRIPT_DIR
/projectnb/wax-es/aramp10/G110_Samples/Scripts/00_Setup_Pipeline
#---------------------------
Job: TopHat_Single_End
ANNOTATION_FILE
RefSeq_GeneBody.gtf
#---------------------------
Job: UCSC_BigWig
VM_DIR_UCSC
/net/waxman-server/mnt/data/waxmanlabvm_home/aramp10/G110
#--------------------------------------------------------------
Check if VM_DIR_UCSC exists:
VM_DIR_UCSC_FASTQC exists!
#--------------------------------------------------------------
#---------------------------
TIME_LIMIT
96:00:00
#--------------------------------------------------------------
DiffExp-specific variables
#--------------------------------------------------------------
#---------------------------
Job: 08a_DiffExp_1_HTSeq
#---------------------------
CONDITION_1_NAME
STAT5_Low
CONDITION_2_NAME
STAT5_High
COMPAR_NUM
1
COUNT_PROGRAM
HTSeq
#---------------------------
Job: 08a_DiffExp_2_HTSeq
#---------------------------
CONDITION_1_NAME
Hypox_male
CONDITION_2_NAME
Hypox_30min
COMPAR_NUM
2
COUNT_PROGRAM
HTSeq
#---------------------------
Job: 08a_DiffExp_3_HTSeq
#---------------------------
CONDITION_1_NAME
Hypox_male
CONDITION_2_NAME
Hypox_90min
COMPAR_NUM
3
COUNT_PROGRAM
HTSeq
#---------------------------
Job: 08a_DiffExp_4_HTSeq
#---------------------------
CONDITION_1_NAME
Hypox_male
CONDITION_2_NAME
Hypox_240min
COMPAR_NUM
4
COUNT_PROGRAM
HTSeq
#---------------------------
Job: 08b_DiffExp_1_featureCounts
#---------------------------
CONDITION_1_NAME
STAT5_Low
CONDITION_2_NAME
STAT5_High
COMPAR_NUM
1
COUNT_PROGRAM
featureCounts
#---------------------------
Job: 08b_DiffExp_2_featureCounts
#---------------------------
CONDITION_1_NAME
Hypox_male
CONDITION_2_NAME
Hypox_30min
COMPAR_NUM
2
COUNT_PROGRAM
featureCounts
#---------------------------
Job: 08b_DiffExp_3_featureCounts
#---------------------------
CONDITION_1_NAME
Hypox_male
CONDITION_2_NAME
Hypox_90min
COMPAR_NUM
3
COUNT_PROGRAM
featureCounts
#---------------------------
Job: 08b_DiffExp_4_featureCounts
#---------------------------
CONDITION_1_NAME
Hypox_male
CONDITION_2_NAME
Hypox_240min
COMPAR_NUM
4
COUNT_PROGRAM
featureCounts
#---------------------------
Job: 08c_DiffExp_1_lncRNA_featureCounts
#---------------------------
CONDITION_1_NAME
STAT5_Low
CONDITION_2_NAME
STAT5_High
COMPAR_NUM
1
COUNT_PROGRAM
featureCounts
#---------------------------
Job: 08c_DiffExp_2_lncRNA_featureCounts
#---------------------------
CONDITION_1_NAME
Hypox_male
CONDITION_2_NAME
Hypox_30min
COMPAR_NUM
2
COUNT_PROGRAM
featureCounts
#---------------------------
Job: 08c_DiffExp_3_lncRNA_featureCounts
#---------------------------
CONDITION_1_NAME
Hypox_male
CONDITION_2_NAME
Hypox_90min
COMPAR_NUM
3
COUNT_PROGRAM
featureCounts
#---------------------------
Job: 08c_DiffExp_4_lncRNA_featureCounts
#---------------------------
CONDITION_1_NAME
Hypox_male
CONDITION_2_NAME
Hypox_240min
COMPAR_NUM
4
COUNT_PROGRAM
featureCounts
#--------------------------------------------------------------
Generate_Tracks:
No parameters to print.
Check that the Sample_Labels.txt has a color column.
#--------------------------------------------------------------
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