Manual for tsRFinder Qinhu Wang and Weixing Shan∗ Northwest A&F University Version 1.0.0 February 11, 2015 Abstract The tsRFinder is a lightweight, fast and reliable tool for prediction and annotation of tRNA-derived small RNAs using next-generation sequencing data. It’s a free open source software available at https: //github.com/wangqinhu/tsRFinder.



Email: [email protected]

1

Contents 1

Introduction

3

2

How to install 2.1 Dependency . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2.2 Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

3 3 3

3

How to use 3.1 Preparing the dataset . . . . . . . . . . . . . . . . . . . . . . . 3.2 Running the pipeline . . . . . . . . . . . . . . . . . . . . . . .

4 4 5

4

Demo 4.1 Demo data . . . . . . . . . 4.2 Demo running . . . . . . . 4.3 Demo output . . . . . . . . 4.4 Visualization of tmap data

5

. . . .

FAQ

. . . .

. . . .

. . . .

. . . .

. . . .

. . . .

. . . .

. . . .

. . . .

. . . .

. . . .

. . . .

. . . .

. . . .

. . . .

. . . .

. . . .

. . . .

. . . .

7 7 8 10 11 13

2

1

Introduction

Small RNAs, such as miRNA, siRNA, and piRNA, are key regulators of gene expression. The tRNA-derived small RNA (tsRNA) is a recently identified novel class of small RNA, no public tool has tailored for tsRNA analysis yet. We thus developed tsRFinder for tsRNA prediction and annotation with additional sequence and statistical analysis, using small RNA sequencing data and the reference genome sequences.

2

How to install

2.1

Dependency

The tsRFinder depends on a few free open source softwares, please check and install them at first: • Perl, v5.10.1 or higher, required for tsRFinder.pl execution. Always build-in in most of the UNIX-like OS. http://www.perl.org/get.html • R, v2.15.2 or higher, required for small RNA data analysis and illustration. http://www.r-project.org • bowtie, v1.0.0 or higher, required for small RNA mapping. https://github.com/BenLangmead/bowtie • tRNAscan-SE, v1.3.1 or higher, required for tRNA prediction. It’s optional if you prefer manual tRNA input. http://lowelab.ucsc.edu/tRNAscan-SE

2.2

Installation

You may clone 1 tsRFinder by typing the following in the terminal. 1

If git is not installed, download it from http://git-scm.com

3

Clone tsRFinder git clone https://github.com/wangqinhu/tsRFinder.git

Alternatively, you may download it from the following URL. Latest release of tsRFinder https://github.com/wangqinhu/tsRFinder/releases/latest

tsRFinder is maintained on GitHub and is ready-to-use, no compilation is required. However, if you take 1 - 2 minutes to improve the configuration, it may save you a lot of time for trouble shooting. Once tsRFinder is cloned or unpacked, move the entire directory to a proper place (or current working directory, such as home directory) and add the tsRFinder path to your environment settings. For example, if tsRFinder is placed in ”/the/path/of/tsRFinder”, then type the following in the terminal if you are using bash. Setup tsRFinder echo export tsR_dir="/the/path/of/tsRFinder" >> $HOME/.bashrc source ˜/.bashrc

tsRFinder is now ready for your dataset, if you want to run tsRFinder.pl as a system command, create a soft link for it: Make a soft link for tsRFinder.pl ln -s ‘pwd‘/tsRFinder/tsRFinder.pl /usr/local/bin/

3 3.1

How to use Preparing the dataset

Before running tsRFinder, you are asked to prepare/download the following two files: (1) the reference genome sequence, or the reference tRNA sequence and, (2) the small RNA reads. You are strongly recommended to use the reference genome sequence and raw small RNA sequencing data since tsRFinder is capable of preparing the reference tRNA data and clean 4

small RNA data automatically. In case you prefer to preparing tRNA and small RNA files manually, see ”demo/tRNA.fas” and ”demo/sRNA.fa.gz” or access the format description in the FAQ section.

3.2

Running the pipeline

Once tsRFinder is properly installed, you can run tsRFinder directly from terminal. A typical tsRFinder job can be easily finished on a modern MacBook (running OS X) or laptop (running Linux), typically within 10 minutes. To know how to use tsRFinder, see the following usage: Usage of tsRFinder: ./tsRFinder.pl -h tsRFinder usage: tsRFinder.pl

Manual for tsRFinder - GitHub

Feb 11, 2015 - Book (running OS X) or laptop (running Linux), typically within 10 min- .... ure (”label/distribution.pdf”) showing the length distributions and base.

325KB Sizes 10 Downloads 177 Views

Recommend Documents

User Manual - GitHub
IIS-1. 0x01C2 2000---0x01C2 23FF. 1K. IIS-0. 0x01C2 2400---0x01C2 27FF. 1K ..... IIS 1 CLOCK REGISTER ...... NFC can monitor the status of R/B# signal line.

The User Manual - GitHub
Defined Wireless Networking Experiments 2017 ..... 1.7.3 Encryption. Mininet-WiFi supports all the common wireless security protocols, such as WEP (Wired Equivalent. Privacy), WPA (Wi-Fi Protected Access) and WPA2. ..... mac80211_hwsim practical exam

TCPCopy Manual - GitHub
Nov 13, 2013 - TCPCopy Manual. Table of Contents. 1 .... online packets at the network layer and does the necessary processing (including TCP ... running online services, the test server is used to do the test tasks and the assistant server is.

OCEMR: User Manual - GitHub
In order to access the program, OCEMR, find the Firefox tab located to the left of the screen. .... click on the view option next to the patient record with the most ..... entered, the report will appear as a download at the bottom of the popup scree

VFS User Manual - GitHub
wind turbines considering the non-linear effects of the free surface with a two-phase .... the nodes of the computational domain are classified depending on their location with ...... bcs.dat need to be set to any non-defined value such as 100.

Reference Manual - GitHub
for the simulation of the electron cloud buildup in particle accelerators. 1 Input files .... points of the longitudinal beam profile of sec- ondary beams.

User Manual - GitHub
Page 1. User Manual. Project Odin. Kyle Erwin. Joshua Cilliers. Jason van Hattum. Dimpho Mahoko. Keegan Ferrett. Page 2. Contents. Contents. Section1 .

GWR4.09 User Manual - GitHub
Starting the program, Exiting the program, and Tab design ...................... 5 ..... GWR4 runs on Windows Vista, Windows 7, 8 and 10 environments with the .

RetroArch Android Manual - GitHub
May 28, 2013 - 7 Core Config Settings. 17. 8 RetroArch on other platforms. 17. 9 About Us. 19. 10 Troubleshooting. 19. 10.1 For non-jailbroken devices only .

Development manual - GitHub
BUSMASTER is located in a Git repository on the open source hosting platform ... version of the installer, e.g. Git-1.7.7-preview20111014.exe (as of 2011-10-26).

installation manual - GitHub
May 8, 2014 - 2. MEGAlib download: It will check if MEGAlib is present. If not it will ..... the source code through the following html file: doc/html/index.html. 9.

SPSToolbox - User Manual - GitHub
May 15, 2013 - Contents. 1 Introduction .... booktitle = {Proceedings of the Automation and Applied Computer Science Workshop ..... System Sciences Series.

Design module user manual - GitHub
In the design module objects like buildings can be selected. For each case, measures ... Figure 3, parts of the web application for control and visualizing data. 1.

RFBee User Manual v1.1 - GitHub
Aug 27, 2010 - 2. 1.2. Specifications. ... 2. 1.3. Electrical Characteristics . ..... >>Datasheet: http://www.atmel.com/dyn/resources/prod_documents/doc2545.pdf. >>Arduino ... >>Datasheet: http://focus.ti.com/docs/prod/folders/print/cc1101.html.