Is CLIP_SAMPLESHEET_TO_BARCODE CLIP-specific?

[samirelanduk]

The module which creates an Ultraplex barcode file from an annotation sheet is currently called CLIP_SAMPLESHEET_TO_BARCODE. There doesn’t seem to be anything specific to CLIP in this in terms of the columns it uses.

Unless there’s something CLIP specific I’ve missed, could it be renamed to simply SAMPLESHEET_TO_BARCODE (or ANNOTATION_SHEET_TO_BARCODE if we’re sticking to the convention that sample sheet = what preprocessing pipelines take to describe already demultiplexes samples and annotation sheet = description of multiplexed file).

[CharlotteAnne]

I agree with your assessment! Again - would you like me to implement?

[chris-cheshire]

Hmm I would disagree a little. The way the python script works feels quite tuned to clip for me. What other protocols use this way to demultiplex barcodes?

[CharlotteAnne]

Again, here ultraplex and the demultiplexing pipeline can theoretically demultiplex any type of sequencing data, just if you're working with very standard things like rna-seq or chip-seq the sequencing facility often perform this step for you.

[samirelanduk]

If it always looks for those three columns and produces a barcode file in the same way each time, I don't see why we would need different modules for different sample types - it's more Ultraplex-specific than sample type specific.

[CharlotteAnne]

if it needs to be extended in future it can be. so should i implement or you @samirelanduk ?

[samirelanduk]

Yes please make the change if we're agreed it's not CLIP-specific, cheers.