From a2c9e26ecbb755de4663782792f18a077aaaadec Mon Sep 17 00:00:00 2001 From: Jian Sheng Boey <95262076+JSBoey@users.noreply.github.com> Date: Fri, 30 Aug 2024 17:25:27 +1200 Subject: [PATCH] Add correct adapters --- docs/day1/ex2_quality_filtering.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/day1/ex2_quality_filtering.md b/docs/day1/ex2_quality_filtering.md index 6a0424d9..55ef2695 100644 --- a/docs/day1/ex2_quality_filtering.md +++ b/docs/day1/ex2_quality_filtering.md @@ -161,7 +161,7 @@ There is a lot going on in this command, so here is a breakdown of the parameter |`mock_R1.qc.fastq.gz`|*positional*|The file to write forward reads which passed quality trimming, if their reverse partner also passed| |`mock_s1.qc.fastq.gz`|*positional*|The file to write forward reads which passed quality trimming, if their reverse partner failed (orphan reads)| |`mock_R2.qc.fastq.gz` / `mock_s2.qc.fastq.gz`|*positional*|The reverse-sequence equivalent of above| - | `ILLUMINACLIP:${adapter}:1:25:7` | *positional* | Adapter trimming allowing for 1 seed mismatch, palindrome clip score threshold of 25, and simple clip score threshold of 7| + | `ILLUMINACLIP:NexteraPE-PE.fa:1:25:7` | *positional* | Adapter trimming allowing for 1 seed mismatch, palindrome clip score threshold of 25, and simple clip score threshold of 7| |`SLIDINGWINDOW:4:30`|*positional*|Quality filtering command. Analyse each sequence in a 4 base pair sliding window and then truncate if the average quality drops below Q30| |`MINLEN:80`|*positional*|Length filtering command. Discard sequences that are shorter than 80 base pairs after trimming|