Question: Processing Gff3 File Of Variants
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gravatar for PaulW
7.8 years ago by
PaulW60
PaulW60 wrote:
Hello all, I have a GFF3 file of variants from nextgen sequencing and want to find non-synonymous changes. Any suggestions? One possible way would be: 1. Use tool "Compute an expression on every row" to extract the reference allele and sample allele from column 9 (attributes column) of the GFF3 file 2. Download some codons (see help for "mutate codons" tool for more info about this) 3. Use the "mutate codons" tool to mutate the codons with the variants extracted from the GFF file. Here is the problem:- The help examples for the tool "compute an expression on every row" are very simplistic. This tool is much more powerful. Where can we find information about how to extract substrings with this tool?
gff • 798 views
ADD COMMENTlink modified 7.8 years ago by Mary Mangan40 • written 7.8 years ago by PaulW60
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gravatar for Mary Mangan
7.8 years ago by
Mary Mangan40
United States
Mary Mangan40 wrote:
Hey guys-- I was trying to move a query to Galaxy today and got this error: http://screencast.com/t/MzUzNzE1ODEt Unable to connect Firefox can't establish a connection to the server at main.g2.bx.psu.edu. I don't know if it's something in UCSC's code or yours, but I thought I would ask. I'm also having trouble getting the site via usegalaxy.org. But we can get there with http://galaxy.psu.edu/ Thanks, Mary Mary Mangan, PhD OpenHelix LLC 65 Main St. Somerville MA 02145 phone: 888-861-5051 x9 http://blog.openhelix.com
ADD COMMENTlink written 7.8 years ago by Mary Mangan40
Hi Mary, We were experiencing some brief server issues which have been resolved. Thanks for reporting this issue! --nate
ADD REPLYlink written 7.8 years ago by Nate Coraor3.1k
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