Sure. The two data files are:

http://test.g2.bx.psu.edu/display?id=23602 http://test.g2.bx.psu.edu/display?id=23607

On Jul 13, 2006, at 10:33 AM, Anton Nekrutenko wrote:

Ross:

Thanks, could you provide links to the data files by clicking on display link and "Copy Link Location" (as shown below).

<Picture 1.png>

anton

Anton Nekrutenko Assistant Professor Department of Biochemistry and Molecular Biology Center for Comparative Genomics and Bioinformatics 505 Wartik Building PennState University University Park, PA 16802 814 865-4752 814 863-6699 FAX anton@bx.psu.edu http://www.bx.psu.edu/~anton http://g2.bx.psu.edu

On Jul 13, 2006, at 10:27 AM, Ross Hardison wrote:

...

The intersection tool under "Operate on Genomic Intervals (bx)" is not working for returning either overlapping regions or overlapping pieces. The intersection and overlaps in the non-bx operations section are working.

I was running intersection (bx) on a set of Mathieu Blanchette's PReMods (118,402 regions) with our RP>0.05 intervals (314,040 regions), in hg17, requiring at least 10bp overlap. Here are the error messages.

For returning overlapping pieces: An error occurred running this job: Traceback (most recent call last): File "./tools/new_operations/gops_intersect.py", line 63, in ? main() File "./tools/new_operations/gops_intersect.py", line 56, in main for line in intersect([g1,g2], pieces=pieces, mincols=mincols): File "

For returning overlapping regions: An error occurred running this job: Traceback (most recent call last): File "./tools/new_operations/gops_intersect.py", line 63, in ? main() File "./tools/new_operations/gops_intersect.py", line 56, in main for line in intersect([g1,g2], pieces=pieces, mincols=mincols): File "

I'll leave the files and results in my history for a while in case that is helpful.

Thanks, Ross

Ross Hardison T. Ming Chu Professor of Biochemistry and Molecular Biology The Pennsylvania State University 304 Wartik Laboratory University Park, PA 16802 e-mail: rch8@psu.edu phone: 814-863-0113 FAX: 814-863-7024

---

Galaxy-user mailing list Galaxy-user@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user

Ross Hardison T. Ming Chu Professor of Biochemistry and Molecular Biology The Pennsylvania State University 304 Wartik Laboratory University Park, PA 16802 e-mail: rch8@psu.edu phone: 814-863-0113 FAX: 814-863-7024