Technology preview of the C1 CAGE protocol: processing and quality control.
HTML Jupyter Notebook
Switch branches/tags
Nothing to show
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
150519_M00528_0125_000000000-ACUAB-links
QC_files/figure-html
output
.gitignore
1772-066-262.imageQC.txt
1772-066-262.picogreen.xlsx
1772-066-263.imageQC.txt
1772-066-263.picogreen.xlsx
LICENSE
OP-WORKFLOW-CAGEscan-short-reads-v2.0.ipynb
QC.Rmd
QC.html
QC.md
README.md
SRM2374_putative_T7_products_NoPolyA_v1.fasta
SimpleArchitecture.txt
Zenbu.md
ercc_and_human_rRNA_and_tagdust.fa
ercc_and_mouse_rRNA_and_tagdust.fa
prerequisite.md
tutorial.md

README.md

Technology preview of the C1 CAGE protocol: processing and quality control.

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.

You will find in this repository:

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.

Authors:

Updates:

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.