search

drivenbyentropy / aptasuite

A full-featured bioinformatics software collection for the comprehensive analysis of aptamers in HT-SELEX experiments.
https://drivenbyentropy.github.io/
GNU General Public License v3.0
24 stars 11 forks source link

reading preprocessed data #100

Closed Jardic closed 2 years ago

Jardic commented 3 years ago

Is it somehow possible to use preprocessed sequences (variable regions only) in whatever format instead of the raw fastq files for aptaClust? I'd find this very useful.

kind Regards Jarda

drivenbyentropy commented 3 years ago

Not quite but this could be be accomplished using the RawReader file format option when parsing the sequence files (one file per selection cycle). This file format simply contains one sequence per line without any additional information. You might however have to add artificial flanking primers to the sequences and specify these in your configuration file (or the import wizard) as I have yet to implement parsing without primers.

Hope this helps!

Jardic commented 3 years ago

Sure, this helps, thank you for the tip!