Can I use a small subset of transcripts as a reference for RNA-seq analysis

[JackMetal]

Instead of using all the transcripts as reference for the RNA-seq analysis, can I use a small subset which I am interested? I compared the results, of course, the expression values from the small subset is higher than that from the whole set. What I'm concerned is that, Does it cause any bias to the expression values?

[dpryan]

This will depend upon how you do your mapping and then the expression quantitation.

[JackMetal]

This will depend upon how you do your mapping and then the expression quantitation.

I used RNA-seq analysis in CLC genomic workbench.
Set parameters is as below
Minimum length fraction: 0.9
Minimum similarity fraction: 0.8
Maximum number of hits for a read: 10
What is the right way to do the mapping and quantitation for a small subset reference? I really appreciate if you can provide a reference for this. Thank you very much!

[NicoBxl]

I don't think it's a good idea. It's always better to map to all the transcript because your data is coming from total RNA ( or poly-A RNA). It can happen that when you map to your subset, some reads maybe map in a better way to transcript that are not in your subset..

[JackMetal]

I don't think it's a good idea. It's always better to map to all the transcript because your data is coming from total RNA ( or poly-A RNA). It can happen that when you map to your subset, some reads maybe map in a better way to transcript that are not in your subset..

Yes, you're right. It is more robust to use entire assembly, since the result would be normalized by the entire mRNA expression, and also much easier for downstream analysis.