RNA-seq for everyone was designed for the RNA-seq beginners in mind.
"A typical RNA-seq experiment consists of the following steps (depicted in figure 3):
- Isolate and purify the starting RNA.
- Convert it to cDNA.
- Convert the cDNA to a library ready for sequencing.
- Sequence using one of the available NGS platforms.
- Analyze the resulting short sequence-reads.
Although all RNA-seq experiments include these steps, there are many experimental details that must be considered before beginning an experiment."
- Insert Size, Strand specific information, if the data is paired ends,
- Adaptor and barcode information used in generating the sequences.
- If read count is same in both fastq files and properly arranged (if paired)
- Number of bases you want to trim in the read, by checking the quality score drop using tools like FASTQC.