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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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Add the ability to import demultiplexed data containing only the randomized region to AptaPLEX #53

Closed drivenbyentropy closed 5 years ago

drivenbyentropy commented 5 years ago
zaklmurray commented 5 years ago

Hi there,

Has this option already been added into the functionality of the software? If not, when do you think it is likely to be added and is there anyway around not having the primer sequences in the data?

Regards, Zak

PJpb commented 5 years ago

Hi, I don't know if you've thought of that, but if you are on hold due to lack of this feature, you can always artificially add some primers to your data.

Also, out of curiosity - how did you get to the point when you've got this data with no primers at all?

Regards, PJ

zaklmurray commented 5 years ago

Hi PJ,

Thanks for your quick reply.

I had thought of adding primers artificially. I have tried it and the tool is working nicely with the artificial primers.

The reason that I got to that point, was that the sequencing supplier provided the data with the primers already trimmed off for some reason. I am going to ask them to send me the raw data as well, as I would like to do the trimming myself.

Cheers, Zak

drivenbyentropy commented 5 years ago

Hi,

As @PJpb has stated, this feature is not available as of yet and the workaround is to add artificial primers. I will look into implementing this and #59 for the next release. Unfortunately I cannot provide an ETA at this moment but I will do my best to be fast.

Thanks!

drivenbyentropy commented 5 years ago

@zaklmurray This feature is now available as of AptaSuite v0.9.1 and above. The parameter AptaplexParser.OnlyRandomizedRegionInData has been added to control this feature (initially set to false). In the GUI you can select this feature under the Advanced Options section of the New Experiment wizard. There you will find it in the Aptamer Properties tab. Please note that this feature is only available if your data is demultiplexed (i.e. one/two file(s) per round depending if paired end or not). The assumption here is that if the primers are missing, so are the barcodes.

Please let me know if you have any further issues and thanks again for suggesting this.

drivenbyentropy commented 5 years ago

Closing 149872af9e244c0d6076b2dbe754d1c2f8c13a22.