User: aviv.de-morgan

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Posts by aviv.de-morgan

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Error in DBA_OLAP_RATE
... Hi, When I try to calculate the overlap rate between peaksets, I get the following errors: > names(broad_gtsf1$masks) # just list all [1] "K562" "H3K9Me3" "75" "313" "WT" "Mutant" "counts" "Consensus" "Replicate.1" "Replicate.2" "Replic ...
diffbind written 5 months ago by aviv.de-morgan0 • updated 5 months ago by Rory Stark2.9k
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Comment: C: DiffBind returns empty consensus peakset
... Thanks, Rory, for your prompt answer. What solved it was passing the path w/o `system.file()` and w/o `package="DiffBind"`. And I do have peaks when I set `minOverlap=4`, which I have to look deeper into. Thanks again. ...
written 5 months ago by aviv.de-morgan0
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DiffBind returns empty consensus peakset
... Dear Rory, I read peaksets to DiffBind as follows: wt <- dba.peakset(NULL, peaks = system.file("/home/labs/shlush/avivdm/chipseq_313_75/9_macs_broad/wt1_ip_chip_7-5.NOMOD_peaks.broadPeak", package = "DiffBind"), peak.caller = "narrow", sampID="WT1_75", tissue = "K562", fa ...
diffbind consensus written 5 months ago by aviv.de-morgan0 • updated 5 months ago by Rory Stark2.9k
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Reading peaks from MACS2 with DiffBind
... The peak format required by DiffBind is BED, whereas MACS2 does not output BED files as MACS14 (the earlier release) did. Rather, it outputs BedGraph (bdg) files, or a variant format of a BED file (see here: https://github.com/taoliu/MACS under Output Files), i.e., the *.narrowPeak or *.broadPeak fi ...
diffbind chip-seq peak calling written 5 months ago by aviv.de-morgan0 • updated 5 months ago by Rory Stark2.9k

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