We are trying to provide users access to the data we have, via the ucsc genome
browser- which I think is the best thing to do because so may people now use
UCSC. The users come to our website and we process a small BedGraph file that
is sent to UCSC and it is then displayed to the user. The problem is that the
bedgraph format does not allow us to do what we want: we want to plot something
like a bar graph or a vertical line which has a height proportional to a
numeric we have (such as number of reads), we also want to display the strand
direction using some thing like the arrows that are allowed for BED files but
seem not allowed for BedGraph files. So my questions are:
1. Is there any format or trick we can use to allow UCSC to display this
information simultaneously?
2. is there anyway to indicate the absolute numeric next to the bar graph?
Basically we want something that could look like this (anything similar would
be just fine - the vertical lines below represent the bar graph):
| reads=20
| | reads=10
Gene p53 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
3. the description of several fields in the microarray track
http://genomewiki.ucsc.edu/index.php/Microarray_track (e.g., thickStart) are
missing, where can we get these info? Basically I am looking for the most
comprehensive bedfile
Thanks
Bino
Asst. Professor
University of Pittsburgh School of Medicine 3080 Biomedical Science Tower 3
3501 Fifth Avenue, Pittsburgh, PA 15260,USA
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