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