Bigbedsummary Output

Question

[GPR]

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.

Answer 1

[Istvan Albert]

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

[GPR]

This is very helpful. Thanks.