July 2006 - galaxy-user - lists.galaxyproject.org

Problem with intersect (bx)
by Ross Hardison 13 Jul '06

13 Jul '06

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(a)psu.edu phone: 814-863-0113 FAX: 814-863-7024

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ENCODE data partioning
by Angelika Merkel 10 Jul '06

10 Jul '06

Hi, I am new Galaxy user and trying to figure out how the ENCODE partitioning works. It says on the webpage that this is based on GENECODE experimentally verified coding sets - is this species specific or a universal prediction? Thanks a lot Angie -- Angelika Merkel Molecular Ecology Lab School of Biological Sciences University of Canterbury Private Bag 4800 Christchurch, New Zealand Ph: ++64 3 364 2987 ext. 7048; 4878

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inconsistent sequences
by Melissa Wilson 06 Jul '06

06 Jul '06

Can anyone help figure out the following problem? I am interested in the exon positions and sequences of EIF1AX. I used Galaxy to find the coding exon positions through UCSC (RefSeq gene NM_001412) using the hg18 (and subsequently hg17 and hg16) sequences. Then I used Fetch Sequences and Alignments to Extract genomic DNA corresponding to query coordinates. The functions work well on the surface, and while there are 435nt extracted for the EIF1AX cds the composition of those 435nt is not the same as the 435nt I get from NCBI NM_001412 CDS nor when I go through UCSC directly to extract the CDS for EIF1AX. This is the same for hg17 and then almost the same for hg16 except for a few additional exons (not clear about those). Perhaps I'm running my search incorrectly, but would someone please check this out. I think a fresh view might clarify things. Best, Melissa

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a suggestion - compressing download files
by Yogeshwar Kelkar 06 Jul '06

06 Jul '06

Hi it takes long time for downloading some huge files from galaxy. how about asking the user whether he/she wants to zip the file before saving / downloading it on local computer? cheers yogeshwar __________________ Yogeshwar Kelkar Makova Lab (517 Mueller University Park, PA 16802)

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Latest genome builds?
by Mike Schaffer 06 Jul '06

06 Jul '06

Hi, It doesn't appear your database has the latest genome builds for human (hg18) and mouse (mm8). Will these be supported soon? Additionally, I was interested in acquiring human/mouse alignments for syntenic introns. When I tried to acquire this from your site for hg17/mm6, it returned a list of alignments, but many of the intron sequences are fragmented across many multiple alignment entries. Is it possible to acquire full "global-like" human/mouse BLASTZ alignments for intron regions from Galaxy, including gapped regions where the sequences aren't alignable? Thanks for any help you can provide. Best regards, Mike Schaffer Ph.D. Candidate Bioinformatics Program Boston University Boston, MA

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