News:Feedback needed on new user-friendly BED file tool

Question

[nadia]

Hi Biostars community,

We've developed a graphical platform that makes working with BED files more intuitive through simple button-click operations. The current version allows you to:

• Merging BED files
• Finding intersections
• Sorting by coordinates
• Extracting regions
• Converting formats (CSV/TSV)

• Basic visualizations

  Would a tool like this save you time compared to command line (BEDTools etc)?

  What crucial features are we missing that would make you actually switch?

  Your suggestions will help us build something actually useful for real work. Thanks in advance for your ideas!

[GenoMax]

While new tools are always welcome (specially if they are easier to use for newcomers) you provide no links for the tool so people can try it out. Please provide links where your software can be accessed for testing.

You could actually convert this post into a tools post and provide more information.

[ATpoint]

Imo you should never reimplement functions that already have long-standing established tools available, unless you can achieve a notable gain in performance. For BED files that would be BEDtools, BEDops, and the wider equivalents in python and R/Bioconductor. If you are into GUIs then wrap these existing tools in such GUI, but reimplementing these tools is (to me) a poor investment of time. That having said, mentioned tools cover the needed range of functions, so use them.

Answer 1

[nadia]

Hello,

I'm sharing a first version of a BED tools platform for community feedback.

Application link: https://bedtools-toolkit.streamlit.app/

The platform accepts files with the .bed extension and currently supports four core operations:

• Preview with file metrics
• Sort by genomic coordinates
• Merge overlapping regions
• Find intersections between sets

The interface is graphical (GUI-based), providing a user-friendly way to perform these operations.

This is an initial version, and feedback on the graphical interface, improvements, usability, and any bugs encountered would be greatly appreciated.

Thank you,

[ATpoint]

What I said already: Don't reimplement, wrap existing tools. I just tried some corrupted files (malformatted), and it threw no errors. It should. Just write a GUI around (py)bedtools, I noted you reimplemented in python. There is really no productive point in that. Do one thing well: Either the underlying codebase or the GUI, but since bedtools already exists that has gone through (community-based and heavy-use) debudding over the last decase, what's the point of going through that again?