A complete guide for analyzing bulk RNA-seq data. Go from raw FASTQ files to mapping reads using STAR and differential gene expression analysis using DESeq2, using example data from Guo et al. 2019.
Hi again! Some of the .sra runs I'm working with seem to have been split into smaller .sra runs. From my understanding, that means I have to merge the .bam files after aligning each of these files. Will this mean I can't use --quantmode geneCounts in STAR because it will count the reads before the bam files get merged? Thank you!
Hi! I noticed that trimming is not part of your RNASeq pipeline. Would you still do quality checks and trimming when analyzing RNASeq datasets that you didn't have sequenced yourself?