[Bioc-devel] [BioC] readGappedAlignments and param argument

[Elena Grassi]

Ok, thanks - I misread the manual, I just thought that was a way to
filter out reads falling over certain regions.
After reading the alignments I use summarizeOverlaps to obtain counts
with the desired options. I decided to use scanBamParam(which=..)
because loading bams and counting overlaps is using a lot of RAM for
big bams and I found online various suggestions to use the
ScanBamParam to load one chr at a time...but as long as I would like
to be general I decided to extract all the seqlevels in the GRanges
object that I'm using and then I would like to iterate over those
extracting the reads that fall on different seqlevels.
I noticed that the counts where different with this approach with
respect to doing all the work together. I guess that I have to find
another way to split my alignments...but I'd really like to avoid
something like:
http://comments.gmane.org/gmane.comp.lang.r.sequencing/755
Reducing my features would not work as long as I need to keep the
original number of the reads...I guess I will have to "flatten" all
the regions falling on a single chr of my Granges in a way that avoid
overlapping reads, that should do the trick (I hope...)...maybe I
could extract the smaller-bigger coords for a given chr and obtain
chr-based Granges from there.

Thank you very much for your help,
E.