drivenbyentropy/aptasuite

Running Aptatrace ignoring primer regions

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shumpeim commented

Hello!

I have very little coding experience, and I was wondering if it was possible to run AptaTrace without the primer regions being involved in structure prediction. My SELEX experiment removed the primer regions in secondary structure formation by incubation with primer-binding oligos. So in motif analysis I'd like that not to be included as well.

Is it possible?

Thanks for any help!

drivenbyentropy commented

Hi @shumpeim,

Thank you for reporting this. As of the latest version of AptaSuite (v0.9.7b), this is now possible by using the new Batch Mode feature. I have updated the wiki accordingly.

While you cannot directly instruct AptaSuite to ignore primers during the secondary structure prediction phase, this can now be accomplished in the following way:

  • Download the newest version of AptaSuite
  • Use AptaSuite’s export function (under Experiment->Export Data) and export all the selection cycles. Make sure that you do not have the ‘primer export’ option checked under Additional Options. Alternatively, you could use any other third party program to demultiplex your data and save the sequences without primers in fastq files (one per selection cycle).
  • Create a new Experiment in AptaSuite and choose IS Demultiplexed and Single End under the Sequencing Information section.
  • In the next window, check the Batch Mode option and follow the reminder of the instructions on screen. When prompted to select the sequencing files for each round, select the ones you exported corresponding to the selection cycle.
  • After importing the sequences, you should be able to perform any analysis within AptaSuite on the primer-less sequences, including running AptaTrace.

Please do let me know if this solves your issue.