Question: Fwd: [Galaxy-Bugs] Help With Mrna Sequences
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gravatar for Anton Nekrutenko
8.5 years ago by
Penn State
Anton Nekrutenko1.7k wrote:
Begin forwarded message: Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org
galaxy • 572 views
ADD COMMENTlink modified 8.5 years ago • written 8.5 years ago by Anton Nekrutenko1.7k
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gravatar for Anton Nekrutenko
8.5 years ago by
Penn State
Anton Nekrutenko1.7k 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
ADD COMMENTlink written 8.5 years ago by Anton Nekrutenko1.7k
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