https://wiki.abi.am/ 2026-04-08T15:48:31+00:00 https://wiki.abi.am/ https://wiki.abi.am/_media/wiki:logo.png text/html 2025-03-11T10:42:03+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.abi.am/talk:scripts:adapter_and_quality_trimming?rev=1741689723&do=diff Quality Control with FastQC and MultiQC Should we create a separate page for FastQC and MultiQC or have them in adapter trimming section? I suggest the following codes: Dauther script fastqc.sh # SCRIPT FOR PERFORMING FASTQC # NOTE: Run this script from the directory where the "log" directory is located, # /mnt/proj/ibd/ds-06_cd-fecal/common # # PURPOSE: # This script performs FastQC. # # PARAMETERS: # 1: input_dir - Directory where FASTQ files are located. # 2: output_dir - Di… text/html 2025-03-11T07:15:06+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.abi.am/talk:scripts:alignment?rev=1741677306&do=diff In the alignment code, I suggest including the -R (read group information) parameter, as it is important for downstream variant calling. Adding it will not interfere with other steps if you are not proceeding with alignment. Here's an example of how to include it: