What are the important information should we know about RNA-seq data file before stating any RNA-seq analysis?

Question

[M K]

What are the important information should we know about RNA-seq data file before stating any RNA-seq analysis for the beginners of this area?

Answer 1

[rtliu]

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):

1. Isolate and purify the starting RNA.
2. Convert it to cDNA.
3. Convert the cDNA to a library ready for sequencing.
4. Sequence using one of the available NGS platforms.
5. 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."

[Istvan Albert]

This is a really nice survey of the library preparation methods.

Answer 2

[Prakki Rama]

• 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.