MGISEQ-2000 adapter trimming

Question

[Alex V. Gopanenko]

Hello community!

I want to take advice regarding proceccing of raw data obtained from MGISEQ-2000. I have 100 PE RNA-seq data.

1. I wonder to know is there any specific features in fastq proceccing comparing with Illumina?

2. I specially want to ask about trimming of adapters. I found sequences below for trimming.

Fwd AAGTCGGAGGCCAAGCGGTCTTAGGAAGACAA

Rev AAGTCGGATCGTAGCCATGTCGTTCTGTGAGCCAAGGAGTTG

What the best way to trim it? What tool better to use and what mode to use?

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Thank you in advance,

Best wishes,

Alex