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parameter_file_description.txt
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Screening parameter file format (take a screening task for 'Glioma_test' as an example):
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Glioma_test
IRIS_data/db/
0.01,0.05,1,0.000001,1 GTEx_Brain
0.000001,0.05,1,0.000001,1 TCGA_GBM,TCGA_LGG
0.01,0.05,1,0.000001,5 GTEx_Heart,GTEx_Skin,GTEx_Blood,GTEx_Lung,GTEx_Liver,GTEx_Nerve,GTEx_Muscle,GTEx_Spleen,GTEx_Thyroid,GTEx_Kidney,GTEx_Stomach
group parametric
False
IRIS_data/resources/mappability/wgEncodeCrgMapabilityAlign24mer.bigWig
IRIS_data/resources/reference/ucsc.hg19.fasta
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Row1 (required): Input group name. This should be identical to the folder name in the IRIS db (see 'format' step)
Row2 (required): Path to the directory of IRIS db
Row3 (see below): Parameters for the tier 1 screening (i.e. 'tissue-matched normal reference')
Fields are separated by ' ': fitler1_cutoffs and filter1_reference_list
within each field, parameters are separated by ',':
- tier1_cutoffs: PSI_p-value_cutoff,deltaPSI_cutoff,FC_cutoff,SJC_p-value_cutoff,filter1_group_cutoff
# PSI_p-value_cutoff: Cutoff of p-value for statistical tests in PSI-based tests.
# deltaPSI_cutoff: Minimum difference of PSI values (i.e deltaPSI) between the tumor and normal tissue in a comparison.
# FC_cutoff: Fold-change cutoff of the PSI value between the tumor and normal tissue in a comparison.
# SJC_p-value_cutoff: Cutoff of p-value for statistical tests in splice junction read count (SJC)-based tests.
# tier1_group_cutoff: Minimum number of tissue-matched normal tissue types in the user-defined reference panel satisfying above requirements. This number should be no larger than the number of reference tissue-matched normal tissue types selected in the next field ('tier1_reference list')
- tier1_reference_list: A list of selected reference panels (separated by ','). Names should be identical to the folder name in the IRIS db (see 'format' step)
Row4 (see below): Parameters for the tier 2 screening (i.e. 'tumor reference'). Same format as the row3
Row5 (see below): Parameters for the tier 3 screening (i.e. 'normal tissue reference'). Same format as the row3
Row3-5 : At least one normal tissue reference panel is required [i.e., tier 1 alone (row 3), or tier 3 alone (row5), or tier 1 + tier 2 + tier 3 (row3-5) are valid settings for screening]. Note that tier 2 alone will not work if tier 1 is missing (tumor recurrence is estabilshed by comparing to a user-specified tissue-matched normal tissue in tier 1)
Row6 (required for PSI-based tests): Comparison mode & statistical test type: 'group' mode (number of input samples >=2) and 'individual mode' (number of input sample =1) are provided. 'group' mode is default and recommended; for PSI-based tests, 'parametric' and 'nonparametric' tests are supported. 'parametric' is default
Row7 (required for PSI-based tests): Use ratio instead of number of groups for the tierX_group_cutoff. Default is False
Row8 (optional): Blocklist file. Removes the AS events that are error-prone due to artifacts. Optional
Row9 (optional): Mappability annotation bigWig file. Required for evaluating splice region mappability.
Row10 (optional): Reference genome file. Required for IRIS translate.
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