The CORALL Data Analysis pipeline includes:The CORALL data analysis pipeline includes:
MultiQC analysis of raw FASTQ files (multiqc V1.5)
UMI extraction
Trimming (Cutadapt V1.18)
FastQC MultiQC analysis of trimmed FASTQ files (FASTQC V0.11.7multiqc V1.5)
Alignment (STAR V2.6.1a)
MultiQC analysis of aligned files (multiqc V1.5)
UMI collapsing (more info can be found here)
Mix² for transcript isoform quantification (Mix² is a Lexogen´s proprietary software; , for more information , please visit our webpage https://www.lexogen.com/mix-analysis-software/?_gl=1*bg2il0*_ga*MjM1NzQ5NTYuMTY2MjEwNjEzMw..*_ga_C4BTKL3CGH*MTY4MjQzODYyNy42NzUuMS4xNjgyNDM4NzAxLjAuMC4w Mix² RNA-Seq Data Analysis Software)
Gene counting (FeatureCounts V1.6.4) > not sure
Differential gene expression analysis (DESeq2 V1.18.1)
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