Sometimes after demultiplexing there exists a high number of undetermined reads, i.e. reads which were not assigned to any library based on the barcodes provided. This is most often the result of incorrect metadata or barcode contamination. Determining what barcodes are present in the undetermined reads can be useful in Read more…
Update 7/21/2021: reform has officially been published as an NFT. Read about this experiment in scientific publishing here. Access the reform publication (PDF) here. Update 11/20/2019: reform is now available as a web app https://reform.bio.nyu.edu/ reform is a python-based command line tool that allows for fast, easy and robust editing Read more…
In this post we will build a pipeline for the HPC using Python 3. We will begin by building the foundation for a pipeline in Python in part 1, and then use that to build a simple NGS analysis pipeline in part 2. At NYU, we submit jobs to the Read more…