Data Process

In the sequencing data processing section, we delve into the essential steps required to prepare raw sequencing data for downstream analyses. This includes quality control (QC) to assess and ensure data integrity, trimming to remove low-quality sequences and adapters, and mapping reads to reference genomes for both RNA and ChIP-seq data. Additionally, I cover file conversion to appropriate formats and proper storage methods to maintain data accessibility and integrity. These preprocessing steps are critical for generating reliable and accurate results in any sequencing-based study.

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Table of contents

• Basal Quality Control with FastQC
• Trimmed reads with Trimmomatic
• Mapping reads with HISAT2 for RNA-seq
• Mapping reads with Bowtie2 for ChIP-seq
• File Conversion and Management with SAMtools
• Feature counts with htseqCount
• File storage with Genozip
• Basal setting and troubleshooting