Alignment

Our primary data contains both single-end and paired-end reads, which are processed slightly differently.

1. Preprocessing

We use NGmerge to remove adapters from paired-end read files, with the parameters: -a -u 41

fastp is used for single-end reads, with these parameters:

--disable_quality_filtering --disable_length_filtering --low_complexity_filter --trim_poly_g

2. Alignment

We align primary data using Bowtie 2 with the following parameters:

Paired-end: --very-sensitive -X 2000 -k 10 --no-discordant --no-mixed --mm

Single-end: --very-sensitive -k 10 --mm