Jun
9
Analyzing RNA-seq data (DEG, Alt. splicing and splicing efficiency analysis)
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.
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.