Dear Sir/Madam, I figured out how to retrieve all conserved human 3'UTR sequences from Table Browser, however they came with multiple repetition (up to 5 times). So my question is “How can I filter these data in order to have all conserved human 3'UTR sequences WITHOUT DUPLICATION THE SAME SEQUEMCES MULTIPLE TIMES?” Sincerely Naum Gershenzon
Dear Naum: You have repetition because of multiple splice variants. There are several options for solving this problem. Option 1 | Merging Intervals ============================ Use Merge tool in "Operate on Genomic Intervals->Merge". This tool will merge all overlapping intervals into a single one. Option 2 | Clustering Intervals =============================== Cluster tool (in "Operate on Genomic Intervals->Cluster") will find overlapping intervals and will allow you to select the largest. To do so, set tool's options to: - "max distance between intervals" to 0 - "min number of intervals per cluster" to 1 - "return type" to "Find the largest interval in each cluster" Let me know if this helps. anton galaxy team On May 1, 2008, at 9:11 AM, Naum Gershenzon wrote:
Dear Sir/Madam,
I figured out how to retrieve all conserved human 3'UTR sequences from Table Browser, however they came with multiple repetition (up to 5 times). So my question is “How can I filter these data in order to have all conserved human 3'UTR sequences WITHOUT DUPLICATION THE SAME SEQUEMCES MULTIPLE TIMES?”
Sincerely
Naum Gershenzon
_______________________________________________ galaxy-user mailing list galaxy-user@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
Naum: See if this movie http://screencast.g2.bx.psu.edu/Nr_3-prime_UTRs.mov clarifies the situation. (You will need quicktime player to watch it). Thanks, anton On May 1, 2008, at 9:11 AM, Naum Gershenzon wrote:
Dear Sir/Madam,
I figured out how to retrieve all conserved human 3'UTR sequences from Table Browser, however they came with multiple repetition (up to 5 times). So my question is “How can I filter these data in order to have all conserved human 3'UTR sequences WITHOUT DUPLICATION THE SAME SEQUEMCES MULTIPLE TIMES?”
Sincerely
Naum Gershenzon
_______________________________________________ galaxy-user mailing list galaxy-user@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
Anton Nekrutenko Asst. Professor Department of Biochemistry and Molecular Biology Center for Comparative Genomics and Bioinformatics Penn State University anton@bx.psu.edu http://nekrut.bx.psu.edu 814.865.4752
participants (2)
-
Anton Nekrutenko
-
Naum Gershenzon