[ NSG QC / trimming ] TrimGalore

nextflow 를 이용하여 RNA-seq을 진행하기 위하여 사용하였다.

 

Trim Galore

Function: FastQ 파일은 일정하게 QC 하고 trimming 하기 위한 툴. warrper tool of Cutadapt and FastQC + some functions for RRBS type library

*Cutadapt: adapter seq, primers, poly-A-tail 등 제거

*FastQC: High throughput sequencing data QC

 

Step 1: Quality Trimming

• low-quality reads trimmed off using phred quality score

Step 2: Adapter Trimming

• Default: 13pb of Illumina standard adapters ('AGATCGGAAGAGC')

Step 3: Removing short sequences

 

(Step 4: specialised trimming)

 

→ output files 을 이용하여 FastQC 실행 가능 (optional)

 

참고

https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/

https://github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md#paired-end-specific-options

https://www.metagenomics.wiki/tools/short-read/quality-control/trim-galore - metagenomic 할 때 유용한 정보 포함