https://divingintogeneticsandgenomics.com/tags/fastqc/ Recent content in Fastqc on Chatomics Hugo -- gohugo.io en-us © 2018 Ming 'Tommy' Tang Fri, 25 Jul 2014 10:53:00 -0700 https://divingintogeneticsandgenomics.com/archive/run-a-local-blast/ Fri, 25 Jul 2014 10:53:00 -0700 https://divingintogeneticsandgenomics.com/archive/run-a-local-blast/ I was checking the quality of a ChIP-seq fastq with fastqc, and the overrepresented sequence showed that the data contain Illumina Single End Adapter 1 contamination. I have a file which contains all the possible illumina library sequences in fasta format (got from here), and I manually looked it and found that the single End Adapter 1 sequence did not match the report. I then was wondering which sequence is the contamination. https://divingintogeneticsandgenomics.com/archive/quality-control-of-your-fastq-file-my-first-post-after-i-got-my-phd/ Thu, 26 Jun 2014 07:06:00 -0700 https://divingintogeneticsandgenomics.com/archive/quality-control-of-your-fastq-file-my-first-post-after-i-got-my-phd/ I passed my defense on Tuesday, and now I am a PhD! what a long process, it took me six years. I've been enjoying the PhD experience though. OK, let me go back to this post. things to remember: 1) You must quality control your fastq files first by fastqc. Trim the adapters and low quality bases by trimmomatic. 2) The fastq files dumped from the SRA GEO repository are usually the raw sequence, you need to quality control them.