Hi, I've tried using the "Operate on Genomic Intervals" tool called "Merge regions of a single query" with some puzzling results. So from the example provided with the tool it seems that if regions fail to merge (i.e. they are unique) then they should be returned in the output along with the merged results, correct? I have used 3 different data files, for human hg18, chimp panTro2, and macaque rheMac2, and each of these files has returned an empty output result. However, they have successfully completed the operation (no error messages were returned). Does this indicate that all regions are unique? Does this indicate a problem with the input file? Does this indicate a problem with the tool?
I have attached an example file.
Thank you for your help, Erika
 ********************************************************** E.M. Kvikstad Academic Computing Fellow IGDP Genetics Center for Comparative Genomics and Bioinformatics The Pennsylvania State University 208 Mueller Lab University Park, PA 16802 (814) 863-2185 kvik@bx.psu.edu
From: Erika kvik@bx.psu.edu Date: September 27, 2006 5:58:47 PM EDT To: galaxy-user@bx.psu.edu Subject: tools: merge regions of a single query
Hi, I've tried using the "Operate on Genomic Intervals" tool called "Merge regions of a single query" with some puzzling results. So from the example provided with the tool it seems that if regions fail to merge (i.e. they are unique) then they should be returned in the output along with the merged results, correct? I have used 3 different data files, for human hg18, chimp panTro2, and macaque rheMac2, and each of these files has returned an empty output result. However, they have successfully completed the operation (no error messages were returned). Does this indicate that all regions are unique? Does this indicate a problem with the input file? Does this indicate a problem with the tool?
Thank you for your help, Erika
********************************************************** E.M. Kvikstad Academic Computing Fellow IGDP Genetics Center for Comparative Genomics and Bioinformatics The Pennsylvania State University 208 Mueller Lab University Park, PA 16802 (814) 863-2185 kvik@bx.psu.edu
Hi Erika,
The Merge tool under the section of "Operate on Genomic Intervals" requires that the input data are in one genome build. It seems like that your data in chr21_NoRecentIRs_NoLowComplx_chimpCoordsOnlyNice.txt are from several builds. That is why you always have error output.
You can try the Merge tool under the section of "Operate on Genomic Intervals(bx)".
Thank you for using of galaxy and providing us the feedback message.
Yi
On Wed, Sep 27, 2006 at 05:58:47PM -0400, Erika wrote:
Hi, I've tried using the "Operate on Genomic Intervals" tool called "Merge regions of a single query" with some puzzling results. So from the example provided with the tool it seems that if regions fail to merge (i.e. they are unique) then they should be returned in the output along with the merged results, correct? I have used 3 different data files, for human hg18, chimp panTro2, and macaque rheMac2, and each of these files has returned an empty output result. However, they have successfully completed the operation (no error messages were returned). Does this indicate that all regions are unique? Does this indicate a problem with the input file? Does this indicate a problem with the tool?
I have attached an example file.
Thank you for your help, Erika
???
E.M. Kvikstad Academic Computing Fellow IGDP Genetics Center for Comparative Genomics and Bioinformatics The Pennsylvania State University 208 Mueller Lab University Park, PA 16802 (814) 863-2185 kvik@bx.psu.edu
Galaxy-user mailing list Galaxy-user@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
Erika,
Use the operations under Operate on Genomic Intervals (bx) javascript:toggle('bxops'). They worked fine for me. However, if you are using main.g2.bx.psu.edu, there was an update to account for an optional strand column that has not yet been implemented in the main galaxy2, so you'll have to input a fake strand column. It doesn't matter for the purposes of merge though...
test.g2.bx.psu.edu works fine without giving a false strand column.
galaxy-user@lists.galaxyproject.org
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Erika -
Ian Schenck -
yizhang＠bx.psu.edu