create a UCSC Track Hub from derfinder results
andrewejaffe opened this issue · comments
it would eventually be nice to have code that takes adjusted coverage, derfinder results, and the genome-wide F-statistic used to find the DERs, and automatically create a UCSC Track Hub. Other inputs would maybe need to be genome build (although it could perhaps be inferred from the genome info on the DERs)
The general structure involves two files called hub.txt and genomes.txt then a folder named as the genome build, which contains BigWigs and bigBeds. These are from my track hub from our nature neuroscience paper: https://s3.amazonaws.com/DLPFC_n36/humanDLPFC/hub.txt . I don't think it would be that hard to at least make a skeleton Track Hub using a simple wrapper.
Example hub.txt
hub humanDLPFC
shortLabel LIBD Human DLPFC Development
longLabel RNAseq data across human brain development by age group from LIBD
genomesFile genomes.txt
email andrew.jaffe@libd.org
descriptionUrl http://www.libd.org
Example genomes.txt
genome hg19
trackDb hg19/trackDb.txt
Then there is a folder called hg19/ that contains trackDb.txt, example:
track DERs
bigDataUrl DERs.bigBed
shortLabel DERs
longLabel Differentially expressed regions (DERs) across brain development
type bigBed 5 .
priority 1
visibility dense
track sixGroup_F
bigDataUrl sixGroup_Fstat_DLPFC_LIBD.bw
shortLabel sixGroup_F
longLabel F-statistic for 36 samples across 6 age groups
type bigWig
priority 2
visibility full
maxHeightPixels 100:32:8
yLineOnOff on
yLineMark 20.51
viewLimitsMax 0:200
viewLimits 0:50
autoscale on
track sixGroupMulti
shortLabel sixGroupDLPFC
longLabel Comparison in human DLPFC across six age groups
container multiWig
aggregate none
showSubtrackColorOnUi on
type bigWig
priority 3
maxHeightPixels 100:32:8
visibility full
yLineOnOff on
yLineMark 5
track FetalOverlay
parent sixGroupMulti
shortLabel Fetal DLPFC
longLabel Normalized RNAseq coverage (Reads/80M) averaged across 6 fetal brains
color 27,158,119
type bigWig
priority 2
bigDataUrl Fetal_DLPFC_LIBD_meanExp.bw
track InfantOverlay
shortLabel Infant DLPFC
longLabel Normalized RNAseq coverage (Reads/80M) averaged across 6 infant brains
parent sixGroupMulti
color 217,95,2
type bigWig
priority 3
bigDataUrl Infant_DLPFC_LIBD_meanExp.bw
track ChildOverlay
parent sixGroupMulti
shortLabel Child DLPFC
longLabel Normalized RNAseq coverage (Reads/80M) averaged across 6 child brains
color 117,112,179
type bigWig
priority 4
bigDataUrl Child_DLPFC_LIBD_meanExp.bw
track TeenOverlay
parent sixGroupMulti
shortLabel Teen DLPFC
longLabel Normalized RNAseq coverage (Reads/80M) averaged across 6 teen brains
color 231,41,138
type bigWig
priority 5
bigDataUrl Teen_DLPFC_LIBD_meanExp.bw
track AdultOverlay
parent sixGroupMulti
shortLabel Adult DLPFC
longLabel Normalized RNAseq coverage (Reads/80M) averaged across 6 adult brains
color 102,166,30
type bigWig
priority 6
bigDataUrl Adult_DLPFC_LIBD_meanExp.bw
track 50plusOverlay
parent sixGroupMulti
shortLabel 50plus DLPFC
longLabel Normalized RNAseq coverage (Reads/80M) averaged across 6 elderly brains
color 230,171,2
type bigWig
bigDataUrl 50plus_DLPFC_LIBD_meanExp.bw
priority 7
http://www.bioconductor.org/packages/release/bioc/html/GenomicInteractions.html could be related to this
@andrewejaffe Doesn't look like this is a much needed feature. Is it ok to close the issue?