Invalid cycle output file [enchancement]

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

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Invalid cycle output file [enchancement] #59

Closed PJpb closed 5 years ago

PJpb commented 5 years ago

Hi, Lately analysing my data I'm having quite a lot of Invalid cycle reads. I'm still wondering and searching if it's my fault or the software's, but that's quite tedious. What would help quite a bit is an output file(s) generate during the parsing, containing all the sequences which were not accepted as correct reads. One could then analyse what went wrong more easily then now. Thanks! :) PJ

drivenbyentropy commented 5 years ago

Hey,

Good idea, and quickly implementable. Will add it in the next version, thanks!

drivenbyentropy commented 5 years ago

This feature is now available in AptaSuite v0.9.1 and above. The wiki has been updated with the parameter AptaplexParser.UndeterminedToFile which is set to false initially. In the GUI this feature is available under the Advanced Options section of the data import wizard.

Files are exported into the export folder and named undetermined_source_file_name.fastq[.gz].

drivenbyentropy commented 5 years ago

Closing 149872af9e244c0d6076b2dbe754d1c2f8c13a22.