The steps I take to analyse RNA-seq data in the lab are :

Checking mapping qualities, e.g. running fastQC on fastq files. Check the fastQ files to see if any reads cotain the primer (adapter sequence). See Note 3 ↓. This could also be seen in the fastQC (quality checking) results (see fig 1 & 2). Remove Illumina primers using a read trimming software, e.g. cutadapt. See Note 4 ↓. This is crucial when the sequenced fragments (High expressed genes) are likely to be shorter than the read length.
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I am a Postdoc researcher at the Neuromuscular Disorders Research lab and Genetic Determinants of Osteoporosis Research lab, in University of Helsinki and Folkhälsan RC. I specialize in Bioinformatics. I am interested in Machine learning and multi-omics data analysis. My go-to programming language is R.
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