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mikpom / uslcount

Quantitation of gene expression from read alignments
GNU General Public License v3.0
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question about this package #1

Open lijing28101 opened 4 years ago

lijing28101 commented 4 years ago

Hi, I'm very interested on your package about correcting the estimation for non-stranded RNA-Seq. I have several questions:

  1. Need I input both stranded and non-stranded bam file for the counting step? If so, it require the same experiment treatment for both library?
  2. You mention to use the junction counts for estimate expression, how to estimate mono-exonic gene? They don't have intron.

Thanks, Jing

mikpom commented 4 years ago

Hi Lijing!

  1. You don't need any stranded library. The package contains pre-trained model which is used every time. Of course concerns can be raised whether this approach is valid for completely unrelated libraries. At least partially we addressed it in the publication by applying the package to other libraries while observing comparable performance.
  2. There is no splice junction insight for monoexonic genes.