Trimmomatic for better quality of FASTQ file

Question

[sruthi]

Hi, I'm new to Trimmomatic and need to trim my FASTQ files using Trimmomatic. The tool provides a default adapter file "TruSeq3-PE.fa". Can this file be considered for the analysis, irrespective of capture enrichment kit used? Or should it be customized? Also, on what basis ahould I set values for LEADING, TRAILING, SLIDINGWINDOW, MINLEN options?

TIA

Answer 1

[lakhujanivijay]

Can this file be considered for the analysis, irrespective of capture enrichment kit used? Or should it be customized?

That really depends on your requirement. Illumina adapter and other technical sequences are copyrighted by Illumina,but Trimmomatic authors have been granted permission to distribute them with Trimmomatic. Suggested adapter sequences are provided for TruSeq2 (as used in GAII machines) and TruSeq3 (as used by HiSeq and MiSeq machines), for both single-end and paired-end mode.

Also, on what basis ahould I set values for LEADING, TRAILING, SLIDINGWINDOW, MINLEN options?

See this link