Query about blacklists

[jantusan]

Hello,

Thank you for developing this tool, I have found it really useful!

I was wondering if you could clarify that use of the --blacklist and --bedsubtract, in particular if they work in a similar way as the DeepTools parameter –blackListFileName. This is the explanation in the help:

 	--blacklist|-c <file>	Input file with list of chromosomes to blacklist during scaling analysis

	--bedsubtract|-u <int>	BED file with regions to subtract when computing coverage for normalization
				These coordinates should not overlap so reads are not counted multiple times

Thank you very much in advance,
Javier

[pongorlorinc]

Hi Javier,

Sorry for the late reply.

The "--blacklist" can be used to specify chromosome names to be excluded for data scaling. Basically, if you want to exclude noisier chromosomes (such as scaffolds or MT DNA), they can be added in here.

The "--bedsubtract" on the other hand gives the option to specify regions that you want to exclude, that may be noisy. Such examples can be centromeric regions, and low mappability regions.

I hope this helps!

Best wishes
Lorinc