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Question: SnpEff output searching for specific genes
2
gravatar for federico.bernuzzi
18 months ago by
federico.bernuzzi • 20
Quadram Institute of BioSciences
federico.bernuzzi • 20 wrote:

Hi,

I have successfully runned SnpEff. The ouput VCF file contains 2.5 million "lines", data sets. I wanted to ask if someone is interested in looking at only a couple of genes how would I go about doing this? In addition is there a chance than the output VCF file can be transported into a different programme for example excel?

Many thanks

FB
rna-seq snp galaxy • 772 views
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modified 18 months ago by Guy Reeves • 1.0k • written 18 months ago by federico.bernuzzi • 20
1
gravatar for Guy Reeves
18 months ago by
Guy Reeves • 1.0k
Germany
Guy Reeves • 1.0k wrote:

maybe you can use 'VCF-BEDintersect:' tool to slice out the genes using their coordinates in a BED file or you can type the interval in. Cheers Guy
ADD COMMENT • link written 18 months ago by Guy Reeves • 1.0k

Agree - another good choice!

ADD REPLY • link written 18 months ago by Jennifer Hillman Jackson ♦ 25k
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gravatar for Jennifer Hillman Jackson
18 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The tool Select can be used to pull out lines that match a specific text string such as a gene ID. There are other data manipulation tools that can filter data by matching text or chromosome coordinates (example: VCFfilter).

VCF is a special version of tabular data, so importing into Excel or other spreadsheet applications is definitely possible. Download the data and change the file extension to be ".txt" or ".tabular". Remove the header before or after downloading or set those lines as a header within the downstream application. The same Select tool can be used to remove header lines in Galaxy ("not matching" the pattern ^#).

Hope this helps! Jen, Galaxy team
ADD COMMENT • link written 18 months ago by Jennifer Hillman Jackson ♦ 25k
0
gravatar for federico.bernuzzi
18 months ago by
federico.bernuzzi • 20
Quadram Institute of BioSciences
federico.bernuzzi • 20 wrote:

Many thanks for the reply I shall look into it.
ADD COMMENT • link written 18 months ago by federico.bernuzzi • 20
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