Quantify_documentation

Quantify is a tool to profile small RNAs like miRNAs,tRNAs, snoRNA etc. in hundreds of single cells simulatenously.

Disclaimer

This tutorial comes with no warranty and demands common sense of the reader. I am not responsible for any damage that happens to your computer by using this tutorial. For comments or questions just create an 'issue' here https://github.com/Drmirdeep/quantify/issues. Apparently you will need a github account for that.

Preface

Quantify is designed to give you a fast overview about the expressed small RNAs in your sequencing files. As input it expects a preprocessed fasta file(s) which need to have a given format. or The first tag ABC123 is and id for the sample or cell which in combination of the second INT tag is a unique identifier for the belonging sequence. The third tag xOCC indicates how often the sequence has been observed in the raw sequencing file e.g. x1000 would indicated that this sequence occurred a 1000 times in the raw file and is present now only once in the preprocessed file. In case you used unique molecular identifiers (UMIs) and want to keep the information in the ID line a fourth tag uOCC can be used for that.

Installation instructions

To obtain the main package from quantify click on 'Clone or download' and then on 'Download Zip'. Extract the zipped files and then open a command line window. If you have git installed you can obtain the packages also directly from the command line by typing To install the quantify package enter the directory to which the package was extracted to. If you extracted the folder on the Desktop then typing will bring you to the quantify_1.0.0 folder. Then typing will start the installer and download and install third party software. In particular. bowtie (version 1), RNAfold, the perl packages PDF:API2 and Font-TTF will be installed. Please follow the instructions (if any) on the screen . When quantify was installed successfully please open a new terminal window and just type You should see the quantify usage page. Download miRBase reference files for version 21 by typing This will download the hairpin.fa.gz and mature.fa.gz for version 21 to directory ~/mirbase/21/

(The ~ sign will be expanded by your computer to your home directory).

If you want the gff files as well then you need to type The second argument can be anything but 0 which will tell the script to also get the gff files from mirbase. Then unzip the files by typing

Data preprocessing for usage with quantify