I'm working with a data set from dbGaP through NCBI, and I'm looking to download some RNA-Seq files. However, there appear to be two different values for Library Selection method to choose from: either PolyA or Hybrid Selection. Some of the samples have just one method or the other, but many have two different RNA-Seq runs, one with each selection method. I guess I'm just looking to get a better idea of the difference between these two.
The protocol description at the top of each run selection page (describing RNA isolation, quality controlling, sequencing techniques, etc.) are exactly identical; the only difference I can see is that the Hybrid Selection runs typically have a slightly higher GC content. If they are the same, why would you need both kinds of run for the same sample? And if they're not the same, what am I missing?
I'm also looking to use these data in conjunction with TCGA data, so if you guys also happen to know which selection method is closer to that used in TCGA sets, that would be greatly appreciated.