From 01f17c014fd813ef81dbf62fa8edc014c4569fd0 Mon Sep 17 00:00:00 2001 From: jsarro13 Date: Tue, 9 Feb 2021 16:14:55 -0500 Subject: [PATCH] Update 03-trimming.md There is no explanation of why the seed mismatch, palindrome clip threshold, and simple clip thresholds are being used. I have added a short non detailed description (lines 138-143 )to avoid any confusion. --- episodes/03-trimming.md | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/episodes/03-trimming.md b/episodes/03-trimming.md index 3ce1625..fcaecec 100644 --- a/episodes/03-trimming.md +++ b/episodes/03-trimming.md @@ -135,13 +135,18 @@ $ cp ~/.miniconda3/pkgs/trimmomatic-0.38-0/share/trimmomatic-0.38-0/adapters/Nex We will also use a sliding window of size 4 that will remove bases if their phred score is below 20 (like in our example above). We will also discard any reads that do not have at least 25 bases remaining after -this trimming step. This command will take a few minutes to run. +this trimming step. Three additional pieces of code are also added to the end +of the ILLUMINACLIP step. These three additional numbers (2:40:15) tell +Trimmimatic how to handle sequence matches to the Nextera adapters. A detailed +explanation of how they work is advanced for this particular lesson. For now we +will use these numbers as a default and recognize they are needed to for Trimmomatic +to run properly. This command will take a few minutes to run. ~~~ $ trimmomatic PE SRR2589044_1.fastq.gz SRR2589044_2.fastq.gz \ SRR2589044_1.trim.fastq.gz SRR2589044_1un.trim.fastq.gz \ SRR2589044_2.trim.fastq.gz SRR2589044_2un.trim.fastq.gz \ - SLIDINGWINDOW:4:20 MINLEN:25 ILLUMINACLIP:NexteraPE-PE.fa:2:40:15 + SLIDINGWINDOW:4:20 MINLEN:25 ILLUMINACLIP:NexteraPE-PE.fa:2:40:15 ~~~ {: .bash}