SEQanswers - View Single Post - Can I use a small subset of transcripts as a reference for RNA-seq analysis

NicoBxl · 09-25-2013, 02:22 AM

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..

09-25-2013, 02:22 AM	#4
NicoBxl not just another member Location: Belgium Join Date: Aug 2010 Posts: 264	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..