Hello,
Is there any idea how we could put the gene name column in the output?
Thanks,
Nikos
Hi @nikomari
Hopefully we can help!
For questions like this
If the input is a bed file, and you want the gene name to pass through a tool, then placing the transcript_id in the bed file is probably where you’ll want to start (4th column). Then, after processing, use the transcript_id as a common key value to join in the gene_id or gene_name.
A gene could be associated with one or more transcripts! A transcript_id has coordinates and is the label used for “processing” steps. Then, later, you can join in other labels! As long as you have the gene_id or gene_name in one column, then the transcript_id in another, you can join into a file that also has one of the keys.
I can let you know that manipulations are very common and there are a few ways to tackle the data merging! Exactly how depends on your files! If you share back what you have, people at this forum will be able to help more!
GTN Tutorials
- Hands-on: Data Manipulation Olympics / Data Manipulation Olympics / Introduction to Galaxy Analyses
- More GTN Materials Search (query=olympics)
If you are starting from bed format, this was originally defined by UCSC, so their specification is a good place to start! They also define gtf so let’s cite that too.
bedGenome Browser FAQgtfGenome Browser FAQ
Suggested tools
- Try exploring the tool panel in the section Text Manipulation
- Or, try a search with keywords like: join, cut, merge
example with “join”
- “interval” is another term for coordinates
- “specified field” means a common keyword value
In short, you’ll need a way to connect data between two or more files. This can be a common key value, or coordinates can be used to join the data based on overlaps and other logical intersections. Columns can be cut out of files and rearranged too! Doing this before graphing is common, to customize the data labels.
Most of these tools are covered in the tutorials, so if the Help on the form is not enough, scroll down into the linked Tutorials to review the how-to more. Any questions, please ask! Seeing the files involved and learning your goals will help us to give advice with more specificity!
Let’s start there, thanks! 
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