From ebf61b03ed24be4eb861ab89ff08cce6db877c2c Mon Sep 17 00:00:00 2001 From: liuqianhn Date: Sun, 28 Jul 2019 10:11:34 -0400 Subject: [PATCH] Update README.md --- day2_alignment/README.md | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/day2_alignment/README.md b/day2_alignment/README.md index 0c5af69..758c925 100644 --- a/day2_alignment/README.md +++ b/day2_alignment/README.md @@ -16,6 +16,15 @@ conda activate base 3. Link reference genome by `ln -s /shared/data/ref_hg37_chr1/ref ref` 4. Link high quality variant file by `ln -s /shared/data/ref_hg37_chr1/vcf vcf` +#### 1.1.1 Check quality of fastq files. +The tool we used is `fastqc`, and you can use the commands below for this purpose. +``` +mkdir -p fastqc_output +fastqc -t 2 -o fastqc_output -f fastq data/sr.chr1.2mb_1.fq data/sr.chr1.2mb_2.fq +``` + +Finally, you will find many new files under `fastqc_output/` for the quality checking. In particular, you will find html files named "XXX_fastqc.html" where "XXX" is the name of the fastq file without `.fastq`. Many useful quality checking could be found in the html file. (We can use a FTP software such as FileZilla to transfer the file from cloud server to local computer to view the html file.) + #### 1.2 Short reads alignment In this tutorial, the reads are from a 2MB region in chr1. We will test two ways to do the alignment.