On Tue, Apr 13, 2010 at 6:42 AM, Hans-Rudolf Hotz <[email protected]> wrote:
> > > On 04/13/2010 03:26 PM, margherita mutarelli wrote: > >> Thank you very much, >> your example was very clear and dissipated my doubts! >> >> This also means that when creating a bed file to be visualized in the UCSC >> browser from an IRanges object, the start column should be converted again >> to 0-index, by subtracting 1 to the start of the coordinates, to visualize >> it correctly, shouldn't it? >> > > And that's exactly what rtracklayer does. It could make your life easier. > yes > > Hans > > > Cheers, >> >> Margherita >> >> >> 2010/4/13 Hans-Rudolf Hotz<[email protected]> >> >> >>> >>> this topic always causes problems. As far as I understand the situation, >>> you have to add 1 to the start of the coordinates you have downloaded (I >>> assume a BED files) from UCSC. >>> >>> Let me try and explain with a simple example: >>> >>> [...] >>> >>> >>> play with the 'upload custom track' (using the small BED file from above) >>> tool on the UCSC genome browser in case this is stil confusing >>> >>> >>> Hans >>> >>> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioc-sig-sequencing mailing list >> [email protected] >> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing >> > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
