Understanding Features of Good Quality: polyA support

[ChrissiKalk97]

I used SQANTI QC on my long read assembly from PacBio HiFi reads.

There is a plot about polyA support in the Features of Good Quality section of the QC report.
I was wondering whether this refers to support in terms of a polyA motif as supplied for the QC run.
I can hardly imagine that it refers to sth else, but just wanted to make sure.

[pabloati]

Hi @ChrissiKalk97, you are completely right. That plot refferes to the percentage of transcripts on each of the main 4 structural categories that has any of the polyA motifs that were supplied to SQANTI3 QC run. This motifs have to be found within the last 50 nucleotides of each transcript to be considered valid by SQANTI3 QC.

I hope this made things clearer and do not hesitate to ask any further quesitons you might have! :)