Problems with dba.analyze in DiffBind - are blacklists/greylists required to obtain DESeq sites?

Question

[bertb]

Hello,

I am trying to perform dba.analyze in DiffBind, but I am unclear on the use of Blacklists/Greylists to obtain differentially bound sites. From my reading of the manual, I thought greylists needed to be set to TRUE to be invoked, though it appears I am attempting to compute a blacklist/greylist (see below)- is this a default setting for dba.analyze?

In any case, while I plan to consider applying a greylist in another analysis, how can I apply the simplest dba.analyze in order to retrieve DESeq sites? Note that I have provided input controls in my sample sheet.

Thanks,

> Bcontrast
6 Samples, 1173 sites in matrix:
    ID Condition Treatment Replicate    Reads FRiP
1 wt1b        WT      none         1 16902874 0.20
2 mt1b        MT      none         1 14594474 0.13
3 wt2b        WT      none         2 16878697 0.22
4 mt2b        MT      none         2 14289354 0.15
5 wt3b        WT      none         3 18699283 0.24
6 mt3b        MT      none         3 15424246 0.20

Design: [~Condition] | 1 Contrast:
     Factor Group Samples Group2 Samples2
1 Condition    MT       3     WT        3
> Bdiff <- dba.analyze(Bcontrast)
Applying Blacklist/Greylists...
Genome detected: Scerevisiae.UCSC.sacCer3
Applying blacklist...
No blacklist found for BSgenome.Scerevisiae.UCSC.sacCer3
Counting control reads for greylist...
Building greylist: C:/Ben/ChIPseq_analyses/bb.202202.ChIPseq/aws/bams/A1.bam
Blacklist error: Error in sample.int(length(x), size, replace, prob): cannot take a sample larger than the population when 'replace = FALSE'

Unable to apply Blacklist/Greylist.
> dba.show(Bdiff, bContrasts=TRUE)
     Factor Group Samples Group2 Samples2
1 Condition    MT       3     WT        3

Answer 1

[Rory Stark]

In the call to dba.analyze(), set bGreylist=FALSE. You can also set bBlacklist=FALSE to avoid seeing the "no blacklist found" message.

You can set these as a configuration parameter in your DBA object so you don't need to specify the parameter everytime you call dba.analyze():

Bcontrast$config$doGreylist  <- FALSE
Bcontrast$config$doBlacklist <- FALSE

[bertb]

Thank you!