Question: Fwd: [Galaxy-Bugs] Help With Mrna Sequences
0
Anton Nekrutenko ♦ 1.7k wrote:
Begin forwarded message:
Anton Nekrutenko
http://nekrut.bx.psu.edu
http://usegalaxy.org
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Anton Nekrutenko ♦ 1.7k wrote:
Lee-Ann:
I shared a history (using chr22 data for simplicity):
http://main.g2.bx.psu.edu/u/aun1/h/mrna-snps-example
and a workflow:
http://main.g2.bx.psu.edu/u/aun1/w/mrna-snps-example
with you that do the trick. Basically, you
1. download mRNA data as BED and as mRNA sequences (history items 1 &
2)
2. Collapse sequences to tab-delimited format (history item 3)
3. Remove dots and numbers by replacing dots with tabs and cutting
accession and sequence out (History items 4 & 5)
4. Join sequences with bed file (History item 6)
5. Downloading the SNPs (History item # 7)
6. Joining with SNPs (History item # 8).
You can use workflow to run this analysis genomewide.
Let me know if you have issues.
Tx,
anton
galaxy team
Anton Nekrutenko
http://nekrut.bx.psu.edu
http://usegalaxy.org
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