Comments (3)
Any news? both positive or negative would be helpful to me.
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I am looking into it now.
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Hi @holgerbrandl,
I've looked into it; there are 9 billion regions in that file. I'm not sure LOLA will be able to do that in its entirety. Do you have any ideas for reducing that?
If you want you can give it a try. This code will split the file into individual bed files for each factor:
wget http://expdata.cmmt.ubc.ca/JASPAR/downloads/UCSC_tracks/2018/mm10/JASPAR2018_mm10_all_chr.bed.gz
mkdir -p mm10/jaspar2018/regions
time zcat JASPAR2018_mm10_all_chr.bed.gz | sed s/[:\.\(\)]/_/g | sed s/__/_/g | awk '{print $_ > "mm10/jaspar2018/regions/"$4".bed"}'
LOLA should be able to load them (see here: http://databio.org/regiondb).
I'm trying this now. But I think if you don't have a lot of memory, that's probably going to be problematic...
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Related Issues (20)
- hg38 database HOT 1
- Add in missing cellType/antibody entries for encodeTFBSmm10 HOT 6
- Re-order result columns
- Different results between LOLAweb interactive server and local R package HOT 7
- cistrome_mm10 HOT 2
- runLOLA results table for PEP databases
- PEP file read caching HOT 2
- Can't load an example regionDB. HOT 3
- PEP tag system
- testing for enrichment of significant individual cpgs HOT 2
- Error if GRangesList has names HOT 2
- question: how to test two region sets for differential enrichment with buildRestrictedUniverse? HOT 2
- Each of the 2 combined objects has sequence levels not in the other: HOT 4
- R package error HOT 4
- LOLA runLOLA-regionDB to use for tissue-specific TFBS
- P4 tool not grouping according to the paper!!
- Error by using extractEnrichmentOverlap function
- Fisher test - two sided hypothesis
- Error when trying to load a regionDB
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