Hi! I am trying to run trust4 using airrflow. I only have single-end read fastq files. Would it be possible to enable airrflow to run single-end read files? Thank you so much!

Hi Obiko, we currently don’t support single-end reads processing with airrflow. I’m not sure whether this is something that @Mark Polster would be interested in implementing

Hi @Obiko and @Gisela Gabernet, the trust4 module is ready for single-end input, so you could run the module outside of the pipeline with your files and then plug the resulting airr files back into the immcantation workflow (this is pretty much whats happening inside the pipeline as well, so no real loss for you wrt to functionality) It's a nice idea to allow single-end files in airrflow directly but I dont think I will find time for this very soon unfortunately

Yes or course I understand, I haven’t seen many single-end protocols for AIRRseq, but there are plenty for bulk RNAseq

Great. Thank you both!!