How to remove extra chromosomes like chrUn_gl00* from pairParam object.

Error in preparePairs("/Users/thimmamp/temp_tobe_deleted/HiCMapped/Dicer1_presplit_out_fixmate.bam",  :
  conversion table should have length equal to the number of chromosomes
> str(hs.param)
Formal class 'pairParam' [package "diffHic"] with 4 slots
  ..@ fragments:Formal class 'GRanges' [package "GenomicRanges"] with 6 slots
  .. .. ..@ seqnames       :Formal class 'Rle' [package "S4Vectors"] with 4 slot

You can remove extra chromosomes in pairParam fairly easily by just removing them in the GRanges object containing the restriction fragment coordinates. For example, to keep only chromosomes 1-19 and X and Y (for the mouse genome, but you get the general idea), you could do something like this:

frags <- mm.param$fragments # where mm.param is a pairParam object
frags <- frags[seqnames(frags) %in% paste0("chr", c(1:19, "X", "Y"))]
mm.param <- reform(mm.param, fragments=frags)

This is only necessary for the release version of diffHic. In the development version, preparePairs is more tolerant of extra chromosomes in the fragment list that aren't in the BAM file, and these will just get ignored (no harm, no foul). In general, though, it's better to construct your fragment list from the same sequences you used for alignment, just to avoid these annoying gotchas. cutGenome should work on one or more FASTA files as well.

In my view, Trisomy, the presence of a third copy of one chromosome, is deleterious and results in invitable or defective progeny if passed through the germ line, with fei2. Using a novel intron-based genetic assay to identify rare homology-independent DNA rearrangements associated with repair of a chromosomal DSB in S. cerevisiae might hele.  Hope it's helpful for you!