Modifying GFF files

Question: Modifying GFF files

16 months ago by

cjain • 10

cjain • 10 wrote:

Hi:

I am working with a GFF file, which is missing 5' UTR annotations. I thought I might be able to add UTR data using the tools on Galaxy as follows:

1) Convert the existing GFF file to Excel format (.xls) using the pencil icon on Galaxy. 2) Download the Excel file and make changes. 3) Upload the modified Excel file and convert it back to GFF using the pencil icon tool. 4) Run HtSeq on RNA-Seq data and the new GFF file to get counts corresponding to each UTR.

However, when I did this the I got no data output. Can anyone suggest what I might have done wrong or how I can modify GFF files using simple tools that do not require bioinformatics expertise?

Thanks,

Chaitanya Jain

rna-seq • 633 views

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modified 16 months ago by Jennifer Hillman Jackson ♦ 25k • written 16 months ago by cjain • 10

16 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

There was probably some format problem introduced when adding in the additional lines, changing the existing content of lines, or in the cycle through Excel (which is notoriously problematic for manipulating and producing plain text output). Even one hidden character (example: a soft return) will cause problems in most bioinformatics pipeline/tools - Galaxy or not.

See the tool in the group Text Manipulation, and the related tool groups immediately below it, in the tool panel at http://usegalaxy.org for data rearrangement options using Galaxy. Many are based on common line-command tools presented through a GUI interface that most should be able to use even with little prior experience. There will always be corner-case manipulations not possible with these tools, but the tools are certainly worth a try, and are from the core original unique features offered in Galaxy. Tools used in combination to achieve complex manipulations, just as one would do in a shell with pipes, are very empowering for non-technical bioinformatic researchers.

Advice:

Make sure that the final dataset meets the specifications of the datatype and is assigned that datatype.
Don't rule out other potential factors, such as a reference genome mismatch problem, until confirmed to be a non-factor. Test the original GFF to confirm that the baseline dataset is working.
Consider finding another data source that includes the missing annotation.
Google to find online datatype format validators. Many are web based and quick to use.
Consider reaching out to a technical colleague, fellow student, and/or co-worker who understands unix tools/data manipulation. What you are attempting is non-trivial and the solution will be specific to your situation.

Help:

https://galaxyproject.org/support/#troubleshooting
In particular, see this FAQ for a list of common problems and fixes and a list of helpful tools: Troubleshoot an error https://galaxyproject.org/support/troubleshoot-an-error/

Thanks, Jen, Galaxy team

ADD COMMENT • link written 16 months ago by Jennifer Hillman Jackson ♦ 25k

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