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added 1) bed->bigBed conversion, 2) QC spreadsheet generation, 3) ENC…
…ODE accession data
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table broadPeak | ||
"BED6+3 Peaks of signal enrichment based on pooled, normalized (interpreted) data." | ||
( | ||
string chrom; "Reference sequence chromosome or scaffold" | ||
uint chromStart; "Start position in chromosome" | ||
uint chromEnd; "End position in chromosome" | ||
string name; "Name given to a region (preferably unique). Use . if no name is assigned." | ||
uint score; "Indicates how dark the peak will be displayed in the browser (0-1000)" | ||
char[1] strand; "+ or - or . for unknown" | ||
float signalValue; "Measurement of average enrichment for the region" | ||
float pValue; "Statistical significance of signal value (-log10). Set to -1 if not used." | ||
float qValue; "Statistical significance with multiple-test correction applied (FDR -log10). Set to -1 if not used." | ||
) |
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table gappedPeak | ||
"This format is used to provide called regions of signal enrichment based on pooled, normalized (interpreted) data where the regions may be spliced or incorporate gaps in the genomic sequence. It is a BED12+3 format." | ||
( | ||
string chrom; "Reference sequence chromosome or scaffold" | ||
uint chromStart; "Pseudogene alignment start position" | ||
uint chromEnd; "Pseudogene alignment end position" | ||
string name; "Name of pseudogene" | ||
uint score; "Score of pseudogene with gene (0-1000)" | ||
char[1] strand; "+ or - or . for unknown" | ||
uint thickStart; "Start of where display should be thick (start codon)" | ||
uint thickEnd; "End of where display should be thick (stop codon)" | ||
uint reserved; "Always zero for now" | ||
int blockCount; "Number of blocks" | ||
int[blockCount] blockSizes; "Comma separated list of block sizes" | ||
int[blockCount] chromStarts; "Start positions relative to chromStart" | ||
float signalValue; "Measurement of average enrichment for the region" | ||
float pValue; "Statistical significance of signal value (-log10). Set to -1 if not used." | ||
float qValue; "Statistical significance with multiple-test correction applied (FDR). Set to -1 if not used." | ||
) |
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table narrowPeak | ||
"BED6+4 Peaks of signal enrichment based on pooled, normalized (interpreted) data." | ||
( | ||
string chrom; "Reference sequence chromosome or scaffold" | ||
uint chromStart; "Start position in chromosome" | ||
uint chromEnd; "End position in chromosome" | ||
string name; "Name given to a region (preferably unique). Use . if no name is assigned" | ||
uint score; "Indicates how dark the peak will be displayed in the browser (0-1000) " | ||
char[1] strand; "+ or - or . for unknown" | ||
float signalValue; "Measurement of average enrichment for the region" | ||
float pValue; "Statistical significance of signal value (-log10). Set to -1 if not used." | ||
float qValue; "Statistical significance with multiple-test correction applied (FDR -log10). Set to -1 if not used." | ||
int peak; "Point-source called for this peak; 0-based offset from chromStart. Set to -1 if no point-source called." | ||
) |
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