From 64898d532828dc814b59211e38aa9b63207428a4 Mon Sep 17 00:00:00 2001 From: Shifu Chen Date: Sun, 4 Feb 2018 17:19:06 +0800 Subject: [PATCH] Update README.md --- README.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 48b4f4a..2b1bb94 100644 --- a/README.md +++ b/README.md @@ -118,7 +118,9 @@ For example, the last cycle of Illumina sequencing is uaually with low quality, * For read2 of PE data, the front/tail trimming settings are given with `-F, --trim_front2` and `-T, --trim_tail2`. But if these options are not specified, they will be as same as read1 options, which means `trim_front2 = trim_front1` and `trim_tail2 = trim_tail1`. # polyG tail trimming -For Illumina NextSeq/NovaSeq data, `polyG` can happen in read tails since `G` means no signal in the Illumina two-color systems. `fastp` can detect the polyG in read tails and trim them. This feature is enabled for NextSeq/NovaSeq data by default, and you can specify `-g` or `--trim_poly_g` to enable it for any data, or specify `-G` or `--disable_trim_poly_g` to disable it. NextSeq/NovaSeq data is detected by the machine ID in the FASTQ records. +For Illumina NextSeq/NovaSeq data, `polyG` can happen in read tails since `G` means no signal in the Illumina two-color systems. `fastp` can detect the polyG in read tails and trim them. This feature is enabled for NextSeq/NovaSeq data by default, and you can specify `-g` or `--trim_poly_g` to enable it for any data, or specify `-G` or `--disable_trim_poly_g` to disable it. NextSeq/NovaSeq data is detected by the machine ID in the FASTQ records.   + +A minimum length can be set with `` for `fastp` to detect polyG. This value is 10 by default. # unique molecular identifer (UMI) processing UMI is useful for duplication elimination and error correction based on generating consensus of reads originated from a same DNA fragment. It's usually used in deep sequencing applications like ctDNA sequencing. Commonly for Illumina platforms, UMIs can be integrated in two different places: `index` or head of `read`.   @@ -196,7 +198,6 @@ options: # polyG tail trimming, useful for NextSeq/NovaSeq data -g, --trim_poly_g force polyG tail trimming, by default trimming is automatically enabled for Illumina NextSeq/NovaSeq data --poly_g_min_len the minimum length to detect polyG in the read tail. 10 by default. (int [=10]) - -G, --disable_trim_poly_g disable polyG tail trimming, by default trimming is automatically enabled for Illumina NextSeq/NovaSeq data # per read cutting by quality options