Entering edit mode
9.1 years ago
Saulius Lukauskas
▴
540
Does anyone have experience with Genboree ?
In particular, how does one translate their analysis report to a particular command that has been run?
The report has been copied here for convenience:
alias: renlab.H3K56ac.hESC.H9.01.01.hg19.level.1.release.3
Analysis Center: EDACC
Analysis File Type: .bed
Analysis File Name: UCSD.H9.H3K56ac.YL238.bed
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 10
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 10 positions it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3
NUMBER_OF_H3K56ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.0217
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.1193
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.5801
IROC_PERCENTILE: 50
POISSON_SCORE: 0.2086
POISSON_PERCENTILE: 100
Namely, this probably must have been something like
pash3 <pash3_parameters> | some_command <some_parameters> | ...
Where pash3_parameters are the ones I am mostly interested in.
