Hi Parick and everybody,
> To everyone, > What other data reduction operations would you like to have on bed file > import? > > > Patrick BED functionality must-haves: well, a very common task is to load all chromosome BED records but segregating by strand. In ChIP-seq analysis for example, an accumulation of forward reads and the left and reverse reads on the right is a good indicator of true peak presence. So, we need to be given the choice of loading "+", "-", or unspecified. The BED specification http://genome.ucsc.edu/goldenPath/help/customTrack.html#BED says that a record without field number 6 (strand) is perfectly valid. Now, regarding the WIG block counting, the user should be able to specify the shiftSize. What's shiftSize? Well, each read is only the end of a DNA fragment that is typically 120 to 200 bases. So, the inferred position of the fragment should the its start position plus 60 to 100 bases. If the fragment matches the reverse strand, then the inferred centre of the fragment should be it 'end' minus 60 to 100. That is the shiftSize. When no strand is specified, the centre of tag should be an acceptable choice. BED functionality to brag about: It would be extremely useful to be able to selectively load BED records contained in a set of genomic regions. (Something like the %in% functionality that Martin recently added to the ShortRead package.) So, lets imagine a tags-containing file and a big regions-containing file. Then we'd do myBigRegions <- import('myBigRegions.bed') insideRegions <- import('myTags.bed', in=myBigRegions, strand=c("+")) or also perhaps outsideRegions <- import('myTags.bed', not_in=myBigRegions, strand=c("+")) Thank you, Ivan Ivan Gregoretti, PhD National Institute of Diabetes and Digestive and Kidney Diseases National Institutes of Health 5 Memorial Dr, Building 5, Room 205. Bethesda, MD 20892. USA. Phone: 1-301-496-1592 Fax: 1-301-496-9878 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
