Question: What are the important information should we know about RNA-seq data file before stating any RNA-seq analysis?
1
gravatar for M K
5.0 years ago by
M K460
United States
M K460 wrote:

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?

rna-seq • 1.9k views
ADD COMMENTlink modified 5.0 years ago by Prakki Rama2.2k • written 5.0 years ago by M K460
6
gravatar for rtliu
5.0 years ago by
rtliu2.0k
New Zealand
rtliu2.0k wrote:

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."

ADD COMMENTlink written 5.0 years ago by rtliu2.0k

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

ADD REPLYlink written 5.0 years ago by Istvan Albert ♦♦ 80k
0
gravatar for Prakki Rama
5.0 years ago by
Prakki Rama2.2k
Singapore
Prakki Rama2.2k wrote:
  • 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. 
ADD COMMENTlink written 5.0 years ago by Prakki Rama2.2k
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