Our purpose here is to provide a bit of guidance to the users of C1 CAGE on Fluidigm's Script Hub, by showing how we align and inspect the data after sequencing.
We hope that this preview will be useful for you to design your experiments and analyses, but please bear in mind that the data used here is just a test run sequenced on MiSeq. A proper publication of the method will follow later.
- A list of software to install first.
- A tutorial on how to process a C1 CAGE library.
- An iPython notebook showing how we processed a pair of C1 runs.
- An example of quality control and prelimnary assessment of the aligned data.
- The license, CC0, under which we release the source code here.
The aligned data was uploaded on the Zenbu genome browser, where it can be visualised as a quantitative expression track. Here is a default view with GENCODE annotation.
- Mickaël Mendez <mickael.mendez@riken.jp>
- Charles Plessy <plessy@riken.jp>
January 2019: Our manuscript is published in Nature communications (Kouno and coll., 2019).
June 2016: Revision B of the C1 CAGE script on Script Hub was released (see below).
May 2016: Updated to new syntax of samtools sort. Will not work with versions
lower than 1.3.
March 2016: the reference sequence of the ERCC spikes has been corrected, see https://www.biostars.org/p/170234/ for details. Following that correction, we detect more spikes in our libraries, and therefore we adjusted our recommended dillution for the RT mixture from 1/200 to 1/20,000. An update on Script Hub will follow.