Problems with dba.analyze in DiffBind - are blacklists/greylists required to obtain DESeq sites?
1
0
Entering edit mode
2.8 years ago
bertb ▴ 20

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
blacklist dba.analyze ChIPseq greylist diffbind • 1.9k views
ADD COMMENT
3
Entering edit mode
2.8 years ago
Rory Stark ★ 2.1k

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
ADD COMMENT
0
Entering edit mode

Thank you!

ADD REPLY

Login before adding your answer.

Traffic: 2421 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6