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
galaxy-user@lists.galaxyproject.org
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Anton Nekrutenko -
Naum Gershenzon