Comments (6)
New version is now deployed here: http://cloud.databio.org/regiondb/
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Oh interesting -- digging a little further, it seems like all of the entries with NAs for cellType and antibody are "RepPeaks" type, meaning they are individual replicates. However, their merged/consensus data ("Peaks") are also present in LOLACore.
For most analyses, one probably wouldn't want to be analysing both the individual replicates and their merged data as though they were independent. It might actually be better to drop these from LOLA?
from lola.
Probably right. But would you rather keep the "RepPeaks" or the individual replicates?
from lola.
I'd rather keep the consensus than the replicates (ie the Peaks rather than the RepPeaks). I've been noticing quite a lot of deviation between replicates, which is presumably why they did them in the first place.
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Thanks for reporting this @oneillkza -- I found 45 extra files in there that shouldn't have been. They had already been excluded from the annotation, but because they were left in the folder, they were still getting read (a feature of LOLA, really...). Anyway, I've taken them out now and will update the public core databases soon. thanks!
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Awesome! Thanks!
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Related Issues (20)
- Re-order result columns
- Different results between LOLAweb interactive server and local R package HOT 7
- Inclusion of mm10 JASAPR prediction track into LOLA JASPAR HOT 3
- 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
- Database download from "latest databases" doesnt work - 403 Forbidden Error HOT 3
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