Hello, and thank you for developing this fantastic tool!
I have generated a GTF file using export_gtf(se_transcript) after running bam_to_tcc() in "de_novo_loose" mode, followed by tcc_to_transcript(). I then applied SQANTI3 for filtering the isoforms in the GTF file. However, I wonder if it might be more effective to apply SQANTI3 filtering at an earlier step, prior to the EM quantification, to ensure that artifact isoforms are not included in the quantification process.
Would you be able to advise on the most appropriate step to run SQANTI3 filtering in this workflow?
Hello, and thank you for developing this fantastic tool!
I have generated a GTF file using
export_gtf(se_transcript)after runningbam_to_tcc()in "de_novo_loose" mode, followed bytcc_to_transcript(). I then applied SQANTI3 for filtering the isoforms in the GTF file. However, I wonder if it might be more effective to apply SQANTI3 filtering at an earlier step, prior to the EM quantification, to ensure that artifact isoforms are not included in the quantification process.Would you be able to advise on the most appropriate step to run SQANTI3 filtering in this workflow?
Kind regards, Sofia