Bioo Scientific offers a complementary qRNASeq script, which eliminates PCR duplicates from RNA-Seq data when Molecular Indexes™ or other stochastic adapters are used during library prep.

Using read pairs aligned to transcripts and Fastq files, this script will generate:

1. a table listing fragments
2. the start/stop sites in transcripts
3. the molecular labels (also known as stochastic labels, or STLs).
4. a table listing total number of read pairs per transcript and number of read pairs after STL, USS, and STL/USS correction

The RNA-Seq script, instructions and a .txt file can be downloaded here.

This program was created by Weihong Xu from the Stanford Genome Technology Center and is supplied with a General Public License (GPL).