Hello, I am gathering the statistics on my RNA-seq data and have ran for this various tools, including bigBedSummary. I have the output in front of me with a list of features, most of which I understand only partially.
These are:
primaryDataSize 806,229,330
primaryIndexSize 5,967,087,257
zoomLevels 10
chromCount: 25
basesCovered 934,386,866
meanDepth 9281.992772
minDepth 2.000000
maxDepth 10441696.000000
std of depth 87164.281564
I am certain of what primaryDataSize and chromCount, but have my doubts about the other features. I tried looking for documentation in the Kent source utilities wiki, but haven't found any useful info.
Some help on this end will be appreciated. G.
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1 answer
I wish these formats were better documented - but that's bioinformatics there. I think we can safely guess what some of these numbers are, and some of them you can easily check relative to your data to make sure that they are right:
primaryDataSize: the number of intervals
primaryIndexSize: some sort of internal representation size (probably used by developers only)
zoomLevels: the internal binning levels used to query intervals (probably used by developers only)
chromCount: number of chromosomes
basesCovered: the number of bases covered
meanDepth: average coverage
minDepth: lowest coverage
maxDepth: maximum coverage
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