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Fastq_clean- version 1.0

Fei lab

Boyce Thompson Institute for Plant Research,

Cornell University,

Tower Road, Ithaca, NY 14853,

United States of America,

Jan 29, 2014

1.Quick start (5)

1.1 Requirements (5)

1.2 Begin with one example (6)

1.3 To clean the paired end sequencing data (7)

2.Parameters (9)

2.1 Required parameter (9)

2.2 Optional parameter (11)

2.3 R script-related options (12)

2.4 BWA-related options (14)

2.5 How to set R script-related parameters (15)

To users:

Fastq_clean is an optimized pipeline to clean the next generation sequencing (NGS) data (DNA-seq or RNA-seq) from the Illumina sequencer. Fastq_clean can also be used to clean the NGS data from other sequencers (e.g. 454), but needs some modification to reach the rest results. The software is available at https://https://www.wendangku.net/doc/c014394279.html,/s/v7sjjmjo56r71k8bvqkv or https://www.wendangku.net/doc/c014394279.html,/s/1sjllrcD for users from china.

The copy right of this software is belonging to the Authors in this published paper[1]. Users can download and use it only for academic purposes with a requirement to cite our published paper. Any commercial use or distribution is not allowed. For any questions or error reports, please contact:

Mi Zhang

Email : zhangmi@https://www.wendangku.net/doc/c014394279.html,

1Quick start

1.1 Requirements

1. This software is supposed to run on the linux system.

2. Perl need be installed, but usually is already pre-installed.

3. R/Bioconductor need be installed.

4. BWA (Version: 0.

5.7 -r1310) and Samtools (Version: 0.1.18) are included in the package.

To install R on the Linux system (Fedora or Ubuntu), please run the first or the second command line as below:

To install Bioconductor in the R environment, please run such command lines:

1.2 Begin with one example

Download fastq_clean-X.Y (X.Y is the version number of the software fastq_clean) from the website. Then, users can start with a published Chrysanthemum RNA-seq dataset including six data files and run such commands as below to learn how to use this software.

1. Download the software folder and rename the working directory “fastq_clean”:

2. Enter the working directory and change the system mode of it:

3. Decompress the database files:

4. Download six data files from the NCBI SRA database into the working directory and transform them into fastq format:

5. Run the pipeline to clean the six data files:

1.3 To clean the paired end sequencing data

In the sample dataset, six fastq files are from the forward end sequencing data. To clean paired end sequencing data, you must provide two fastq file list and run the pipeline twice for forward end sequencing and reverse end sequencing data.

2Parameters

There are four categories of parameters: required, optional, R script-related and BWA-related. Users can run the command line “./fastq_clean.pl” to see all the parameter description.

2.1 Required parameter

--file_list

The fastq_clean program is designed to process input files in batch, so a text file should be provided to include a list of input file names (the first column) and the corresponding 3’ adapter sequences (the second column). The first column in the file list can only include the base names of the input files (see the figure 1) without suffix names.

Fig 1. The content of fastqfiles1.list

In the working directory, a file named “fastqfiles1.list”was included to

clean the sample dataset (see the figure 1). The 3’ adapter sequences are from TruSeq RNA Sample Preparation Kits, which covers more than 80% usage in RNA-seq and also used in some DNA-seq application. Users can simply replace the first column with their own data file names and replace the second column with their own adapter sequences to run this pipeline on their own data.

Fig 2. The arrangement of the working directory

The corresponding input files in the list must be included in the working directory with suffix name “.fastq”. All the input files must be the raw data from the sequencer. The raw data having lines of the same length should not be processed by any data clean programs.

2.2 Optional parameter

--run_R

To run the R script to remove low quality, ambiguous and adapter bases in the input data. The default setting is to run the R script.

--rRNA_removal

To run the Perl script to remove reads which can be aligned to the rRNA reference sequences.

--rRNA_reference

If the parameter “rRNA_removal”is set, an rRNA reference database named rRNA_silva111.fasta in FASTA format should be provided in the folder $work_dir/databases.

--virus_removal

To run the Perl script to remove reads which can be aligned to the virus reference sequences.

--virus _reference

If the parameter “virus_removal” is set, a virus reference database named vrl_genbank.fasta in FASTA format should be provided in the folder $work_dir/databases.

2.3 R script-related options

--pattern_file

The name of a file containing a list of adapter pattern strings. There are two pattern files “patterns_forward”and “patterns_reverse”in the working directory. They are designed to remove some other contamination in the forward and reverse sequencing data after removing the low quality, ambiguous and adapter bases. These patterns are also from TruSeq RNA Sample Preparation Kits.

--quality_Cutoff

Low quality bases below this parameter will be trimmed from both ends of reads. The default value is 20, which is the most common used in quality control.

--region_5Len

The low quality region from the 5' end of reads. The default value is10. The

“region_5Len”, “region_3Len”, and “n_Cutoff”are optimized for the illumine 100bp sequencing technology.

--region_3Len

The low quality region from the 3' end of reads. The default value is 20.

--n_Cutoff

After low quality bases trimmed, the reads containing "N" with a number above this parameter will be removed. The default value is 2.

--adapter_mismatch

A mismatch ratio between adapters with the 3' ends of reads. The default value is 0.1.

--read_Length

Reads with the length shorter than this parameter will be removed. The default value is 25.

--read_PerYield

Number of reads processed in each iteration to limit the memory usage. The default value is 5e5.

2.4 BWA-related options

--max_dist Maximum edit distance [1]

--max_open Maximum number of gap opens [1]

--max_extension Maximum number of gap extensions [1]

--len_seed Take the first INT subsequence as seed [36]

--dist_seed Maximum edit distance in the seed [1]

--thread_num Number of threads (multi-threading mode) [8]

This pipeline uses the BWA program[2] to align reads to the virus or rRNA reference sequences. To call the BWA program in the command line, six parameters (“n”, “o”, “e”, “l”, “k”,“t”) need be set and renamed by (“max_dist”, “max_open”, “max_extension”, “len_seed”, “dist_seed”, “thread_num”). For detailed description of those parameters, users can see the online manual of the program BWA (https://www.wendangku.net/doc/c014394279.html,/bwa.shtml).

2.5 How to set R script-related parameters

The “region_5Len”, “region_3Len”, and “n_Cutoff” parameters (see 2.3) are optimized for the illumine 100bp sequencing technology. For seq data of other length, users must set these parameters by themselves. Table 1 provides some recommended parameters for user’s convenience.

Table 1. parameters for seq data of different length

3Runtime Errors

Input file having line of different length

Error in replaceLetterAt(seqs, at, letter) :

'x' must be rectangular (i.e. have a constant width)

1. Xu, Y., et al., Transcriptome sequencing and whole genome expression profiling of

chrysanthemum under dehydration stress. BMC Genomics, 2013. 14(1): p. 662.

2. Li, H. and R. Durbin, Fast and accurate short read alignment with Burrows-Wheeler transform.

Bioinformatics, 2009. 25(14): p. 1754-1760.

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User Manual Dear Customers, Welcome to your smart wristband. The smart wristband, a device that measures your daily job and activity with quality products and services. With this device, you can actually experience the excellence and humanization design of the device. Bring you a pleasant and enjoyable life. Thanks for choosing us, we provide the particular instructions for better operating the products. Before using the products, please read the instruction first. If there is any misprint, please do understand. Thank you. 1 .Product Description With the high-end and well-designed appearance, the portable multifunctional smart wristband is perfect in: tracking steps, distance measurement, calorie consumption management, monitoring your sleep cycle, time displaying, waking you (for drinking, sitting for too long, waking

User manual

UM0462 User manual STM32? and STM8? Flash loader demonstrator Introduction The purpose of this document is to describe the STMicroelectronics STM32? and STM8? Flash loader demonstrator application that was developed to illustrate the System memory boot loader capabilities. This document details the prerequested hardware and software environments, as well as the use cases of the demonstrator software. November 2009Doc ID 13916 Rev 71/25 https://www.wendangku.net/doc/c014394279.html,

Contents UM0462 Contents 1Getting started . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 1.1Package contents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 1.1.1Software contents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 1.1.2Hardware contents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 1.2System requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 1.3Flash loader demonstrator installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 1.3.1Software installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 1.3.2Hardware installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 2User interface description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10 3Command-line usage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20 4Revision history . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24 2/25 Doc ID 13916 Rev 7

UserManual

AdView iOS SDK 开发者手册 v1.4.4

AdView iOS SDK 介绍 AdView iOS SDK是专为iOS开发者免费提供的移动广告优化工具，旨在帮助开发者轻松实现广告收益最大化。基于广告聚合的应用互推，帮助应用迅速扩大用户数。同时我们联合多家广告平台和应用商城，开通绿色通道服务，为广大开发者服务。 AdView iOS SDK 包含如下内容: 文件或目录名说明 AdNetworks AdView SDK 支持的广告平台开发包. AdView.framework AdView SDK 开发包. Resources AdView SDK 依赖的资源文件. SBJson部分广告平台依赖的 json-framework 源代码. TouchJSON部分广告平台依赖的 TouchJSON 源代码. JSONKit部分广告平台依赖的 JSONKit 源代码.

在项目中集成 AdView 在项目中集成 AdView 比较容易, 通常您按照以下步骤即可把 AdView 集成到您的项目中. 1.从网站获取 AdView SDK 开发包, 在 Finder 中解压. 您将在 Finder 中看到解压后的 AdView SDK. 如图所示. 2.在 Xcode 中打开您的工程. 在此以 AdView SDK 所附带的 AdViewHello 工程为例.

3.在 Finder 中把 AdViewSDK 目录拖到 AdViewHello 工程中. 4.在 Xcode 弹出的对话框中选中 “Copy items into destination group’s folder (if needed)”. 完成以后 AdView SDK 即已经添加到项目中. 如图所示. 5.AdView SDK 开发包附带了所有支持的广告平台. 但是不幸的是某些广告平台之间会有?一些符号冲突. 所以您不得不忍痛割爱?一些广告平台. 这些广告平台的冲突主要有:

QTLNetworkUserManual

QTLNetwork-2.0 User Manual Software for Mapping QTL with Epistatic and QE Interaction Effects Jian Yang, Chengcheng Hu, Xiuzi Ye and Jun Zhu Copyright 2005-2006 ? Zhejiang University, China This software can be freely redistributed with non-commercial purpose and under the condition of no changes to the software and its related documents. No warranty of any sort is provided for use of the software.

Contents QTLNetwork-2.0 User Guide (1) 1. Introduction to QTLNetwork (3) 2. Installing QTLNetwork (3) 3. Running QTLNetwork (6) 4. Starting with QTLNetwork (7) 4.1. Data Format (7) 4.2. Create new project with map and data files (13) 4.3. Open the project with map, data and result files (21) 5. Interactive Visualization operations (22) 6. Config setting in the mapping computation (23) 6.1. General page (24) 6.2. Genome scan configuration page (25) 6.3. Significance level configuration page (25) 6.4. Output configuration page (26) 7. Graph setting (26) 8. Save pictures and reports (27) 8.1. Save pictures (27) 8.2. Save and understand the text reports (27)