Good morning Sean and everybody, > > Actually, the edge case is general as alignments, even on linear > chromosomes, may extend beyond the end of the chromosome, I believe. > In the best case, these alignments are clipped (in CIGAR terms), but I > don't know that all aligners are doing that appropriately. > > Sean
So, you rather go for an overriding switch rather than infrastructure overhaul? I ask this because GRanges is an exceptionally convenient format for ChIP-seqers and Patrick is trying to make a decision to make it work for real world data. And yes indeed: aligners do align a little bit past the boundaries even for linear chromosomes. Thanks for pointing that out! Ivan _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
