转录组入门3：了解fastq测序数据

目的：用安装好的sratoolkit把sra文件转换为fastq格式的测序文件，并且用fastqc软件测试测序文件的质量。
作业：理解测序reads，GC含量，质量值，接头，index，fastqc的全部报告，搜索中文教程

一. SRA Toolkit官方文档

https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc

Frequently Used Tools:

fastq-dump: Convert SRA data into fastq format
prefetch: Allows command-line downloading of SRA, dbGaP, and ADSP data
sam-dump: Convert SRA data to sam format
sra-pileup: Generate pileup statistics on aligned SRA data
vdb-config: Display and modify VDB configuration information
vdb-decrypt: Decrypt non-SRA dbGaP data ("phenotype data")

Additional Tools:

abi-dump: Convert SRA data into ABI format (csfasta / qual)
illumina-dump: Convert SRA data into Illumina native formats (qseq, etc.)
sff-dump: Convert SRA data to sff format
sra-stat: Generate statistics about SRA data (quality distribution, etc.)
vdb-dump: Output the native VDB format of SRA data.
vdb-encrypt: Encrypt non-SRA dbGaP data ("phenotype data")
vdb-validate: Validate the integrity of downloaded SRA data

SRA Toolkit Installation and Configuration Guide

Testing the Toolkit configuration

download repository(Linux): /home/[user_name]/ncbi/public
For the test, we are using an arbitrary dataset, S