Dear All
I am using qiime2 for analysing my 16S rRNA gene sequence data (single end), generated from IonS5 sequencer. I want to select reads of particular length (200 - 300 bps) for my further analysis. But I am unable to do so during sequence quality control and feature table construction using DADA2. Could you please suggest the best way to do it. Also, if possible suggest the same for Debular as well.
I have used this command as mentioned below
There is a QIIME 2 plugin called RESCRIPt (which needs to be installed separately, follow instructions at the link below). It has an action for filtering sequences by both minimum and maximum lengths:
This will need to be run after denoising, however, so may or may not help your use case.
This will truncate all reads at position 200, and filter out any that are shorter. But indeed this will not filter out reads that are too long (it will only trim them).
