Hi 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!

Unsure, James, let me try to answer

I use BED files frequently in my bioinformatics work, primarily through command-line tools like BEDTools and bedops. A graphical platform with button-click operations would not save me time compared to the command line, as I am proficient with scripting and find it faster for batch processing and integration into pipelines. For example, merging BED files can be done efficiently with:

bedtools merge -i input.bed > output.bed

However, such a tool might benefit less experienced users who struggle with syntax.

Crucial missing features that would make me consider switching include:

• Support for subtracting regions between BED files, equivalent to bedtools subtract.
• Complement operations to find genomic regions not covered by input intervals.
• Closest feature identification, like bedtools closest.
• Integration with BAM/SAM files for coverage calculations.
• Advanced filtering based on custom criteria, such as overlap percentages or strand-specific operations.
• Export to additional formats like GFF3 or BigBed.
• Scripting interface to allow automation and reproducibility, perhaps via generated command-line equivalents.
• Handling of large files without performance issues, including parallel processing.
• Statistical analysis of intervals, such as enrichment tests.

Without these, the tool remains too basic for complex analyses.

Kevin