I have mapped my data to drosophila genome BDGP6.28. Hence, the bam files and peaks' chromosome names are 2L, 2R, 211000022278421, 211000022278482, et cetera. When I try to filter blacklists with dba.blacklist function
dba.blacklist(dbObj_initial, blacklist = DBA_BLACKLIST_DM6, greylist=FALSE)
I am informed that no blacklists are found, even though I have looked at the peaks, and saw that some do fall at blacklists' area from here.
More importantly, when I try to use greylists
dba.blacklist(dbObj_initial, blacklist = FALSE, greylist=DBA_BLACKLIST_DM6) Error in value[[3L]](cond) : GreyListChIP error: Error in tileGenome(obj@karyotype, tilewidth = tileSize/2): 'seqlengths' contains NAs or negative values
I think both issues stem from the difference in chromosome names - in my peaks (and in my bam files) the chromosome names do not have "chr", and I guess that in the chromosome names DiffBind uses they do.
Is it possible to circumvent it and what would it take?
I can clean the blacklisted peaks by myself, using bedtools; but when it comes to greylists, I would be glad to enjoy the automatic use of greylists in DiffBind.
Is there any solution for it (perhaps using the diffloop package)?