nebnext single cell rna seq templete switching oligo and G and T homopolymers trimming.

[sunta3iouxos]

Hi all, Any recommendations on how to trim the generated fastq files from this library using fastP? The default options can not automatically recognize the adapters. The adapters used are described HERE. In this page they recommend using FlexBar. Flexbar first will remove the switching oligo and also G and T homopolymers using the following options:

Homopolymers adjacent to the template-switching oligo are trimmed as well, as specified by --htrim* options. G and T homopolymers are trimmed (--htrim-left GT --htrim-right CA). Homopolymer length to trim is 3-5 for G, and 3 or higher for T (--htrim-min-length 3 --htrim-max-length 5 --htrim-max-first).
Keeping a short minimum read length after trimming (--min-read-length 2) keeps informative long reads, whose mates may be short after trimming. 

Then it will proceed on trimming the illumina adapters.

I am unsure how this can be adjusted for fastp and also how can fastp handle those 2 steps.

Thank you all in advance.