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?
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Originally posted by dpryan View PostThis will depend upon how you do your mapping and then the expression quantitation.
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!
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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..
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Originally posted by NicoBxl View PostI 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..
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