Question: SnpEff output searching for specific genes
2
gravatar for federico.bernuzzi
6 months ago by
Quadram Institute of BioSciences
federico.bernuzzi20 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 • 250 views
ADD COMMENTlink modified 6 months ago by Guy Reeves1.0k • written 6 months ago by federico.bernuzzi20
1
gravatar for Guy Reeves
6 months ago by
Guy Reeves1.0k
Germany
Guy Reeves1.0k 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 COMMENTlink written 6 months ago by Guy Reeves1.0k

Agree - another good choice!

ADD REPLYlink written 6 months ago by Jennifer Hillman Jackson23k
0
gravatar for Jennifer Hillman Jackson
6 months ago by
United States
Jennifer Hillman Jackson23k 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 COMMENTlink written 6 months ago by Jennifer Hillman Jackson23k
0
gravatar for federico.bernuzzi
6 months ago by
Quadram Institute of BioSciences
federico.bernuzzi20 wrote:

Many thanks for the reply I shall look into it.

ADD COMMENTlink written 6 months ago by federico.bernuzzi20
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