20220912-0919 转录组-CFANZ编程社区

软件安装fastp ascp 数据下载处理质控

anaconda3下载安装配置

channels:
  - http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/
  - http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/
  - http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/
  - http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/pytorch/
  - http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/menpo/
  - http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/msys2/
  - http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/
show_channel_urls: true
auto_activate_base: true

fastp安装 conda install fastp

fastp 安装问题及解决方法 - 简书 (jianshu.com)

aspera wget https://www.ibm.com/support/fixcentral/swg/doSelectFixes?options.selectedFixes=ibm-aspera-connect_4.2.2.135_linux.tar&continue=1

文件的压缩解压 tar -zxvf 文件 tar -zcvf 文件 sh/bash .sh

ascp下载数据(备份）

1. NCBI数据下载

ascp -i ~/.aspera/connect/etc/asperaweb_id_dsa.openssh -l 100M -k 1 -T anonftp@ftp.ncbi.nlm.nih.gov:/refseq/release/viral/viral.2.1.genomic.fna.gz .

2.EBI数据下载

ascp -i ~/.aspera/connect/etc/asperaweb_id_dsa.openssh -l 100M -T -P33001 fasp-g1k@fasp.1000genomes.ebi.ac.uk:vol1/ftp/release/20100804/ALL.2of4intersection.20100804.genotypes.vcf.gz .

aspera下载srr

密钥地址： /home/ubuntu/anaconda3/envs/bioinfor/etc/asperaweb_id_dsa.openssh

paper： Transcriptome analysis of an apple (Malus × domestica) yellow fruit somatic mutation identifies a gene network module highly associated with anthocyanin and epigenetic regulation PRJNA287523/SRP062637 ENA下载 ENA Browser (ebi.ac.uk)

ascp -l 100M -P 33001 -QT -k 2 -i /home/james/.aspera/connect/etc/asperaweb_id_dsa.openssh era-fasp@fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/008/SRR2176358/SRR2176358.fastq.gz /home/james/rnaseq/rawdata
ascp -l 100M -P 33001 -QT -k 2 -i /home/james/.aspera/connect/etc/asperaweb_id_dsa.openssh era-fasp@fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/009/SRR2176359/SRR2176359.fastq.gz /home/james/rnaseq/rawdata
ascp -l 100M -P 33001 -QT -k 2 -i /home/james/.aspera/connect/etc/asperaweb_id_dsa.openssh era-fasp@fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/000/SRR2176360/SRR2176360.fastq.gz /home/james/rnaseq/rawdata
ascp -l 100M -P 33001 -QT -k 2 -i /home/james/.aspera/connect/etc/asperaweb_id_dsa.openssh era-fasp@fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/001/SRR2176361/SRR2176361.fastq.gz /home/james/rnaseq/rawdata
ascp -l 100M -P 33001 -QT -k 2 -i /home/james/.aspera/connect/etc/asperaweb_id_dsa.openssh era-fasp@fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/002/SRR2176362/SRR2176362.fastq.gz /home/james/rnaseq/rawdata
ascp -l 100M -P 33001 -QT -k 2 -i /home/james/.aspera/connect/etc/asperaweb_id_dsa.openssh era-fasp@fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/003/SRR2176363/SRR2176363.fastq.gz /home/james/rnaseq/rawdata
ascp -l 100M -P 33001 -QT -k 2 -i /home/james/.aspera/connect/etc/asperaweb_id_dsa.openssh era-fasp@fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/004/SRR2176364/SRR2176364.fastq.gz /home/james/rnaseq/rawdata
ascp -l 100M -P 33001 -QT -k 2 -i /home/james/.aspera/connect/etc/asperaweb_id_dsa.openssh era-fasp@fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/005/SRR2176365/SRR2176365.fastq.gz /home/james/rnaseq/rawdata
ascp -l 100M -P 33001 -QT -k 2 -i /home/james/.aspera/connect/etc/asperaweb_id_dsa.openssh era-fasp@fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/006/SRR2176366/SRR2176366.fastq.gz /home/james/rnaseq/rawdata
ascp -l 100M -P 33001 -QT -k 2 -i /home/james/.aspera/connect/etc/asperaweb_id_dsa.openssh era-fasp@fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/007/SRR2176367/SRR2176367.fastq.gz /home/james/rnaseq/rawdata
ascp -l 100M -P 33001 -QT -k 2 -i /home/james/.aspera/connect/etc/asperaweb_id_dsa.openssh era-fasp@fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/008/SRR2176368/SRR2176368.fastq.gz /home/james/rnaseq/rawdata
ascp -l 100M -P 33001 -QT -k 2 -i /home/james/.aspera/connect/etc/asperaweb_id_dsa.openssh era-fasp@fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/009/SRR2176369/SRR2176369.fastq.gz /home/james/rnaseq/rawdata
ascp -l 100M -P 33001 -QT -k 2 -i /home/james/.aspera/connect/etc/asperaweb_id_dsa.openssh era-fasp@fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/000/SRR2176370/SRR2176370.fastq.gz /home/james/rnaseq/rawdata
ascp -l 100M -P 33001 -QT -k 2 -i /home/james/.aspera/connect/etc/asperaweb_id_dsa.openssh era-fasp@fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/001/SRR2176371/SRR2176371.fastq.gz /home/james/rnaseq/rawdata
ascp -l 100M -P 33001 -QT -k 2 -i /home/james/.aspera/connect/etc/asperaweb_id_dsa.openssh era-fasp@fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/002/SRR2176372/SRR2176372.fastq.gz /home/james/rnaseq/rawdata
ascp -l 100M -P 33001 -QT -k 2 -i /home/james/.aspera/connect/etc/asperaweb_id_dsa.openssh era-fasp@fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/003/SRR2176373/SRR2176373.fastq.gz /home/james/rnaseq/rawdata
ascp -l 100M -P 33001 -QT -k 2 -i /home/james/.aspera/connect/etc/asperaweb_id_dsa.openssh era-fasp@fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/004/SRR2176374/SRR2176374.fastq.gz /home/james/rnaseq/rawdata
ascp -l 100M -P 33001 -QT -k 2 -i /home/james/.aspera/connect/etc/asperaweb_id_dsa.openssh era-fasp@fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/005/SRR2176375/SRR2176375.fastq.gz /home/james/rnaseq/rawdata
ascp -l 100M -P 33001 -QT -k 2 -i /home/james/.aspera/connect/etc/asperaweb_id_dsa.openssh era-fasp@fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/006/SRR2176376/SRR2176376.fastq.gz /home/james/rnaseq/rawdata
ascp -l 100M -P 33001 -QT -k 2 -i /home/james/.aspera/connect/etc/asperaweb_id_dsa.openssh era-fasp@fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/007/SRR2176377/SRR2176377.fastq.gz /home/james/rnaseq/rawdata
ascp -l 100M -P 33001 -QT -k 2 -i /home/james/.aspera/connect/etc/asperaweb_id_dsa.openssh era-fasp@fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/008/SRR2176378/SRR2176378.fastq.gz /home/james/rnaseq/rawdata
ascp -l 100M -P 33001 -QT -k 2 -i /home/james/.aspera/connect/etc/asperaweb_id_dsa.openssh era-fasp@fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/009/SRR2176379/SRR2176379.fastq.gz /home/james/rnaseq/rawdata
ascp -l 100M -P 33001 -QT -k 2 -i /home/james/.aspera/connect/etc/asperaweb_id_dsa.openssh era-fasp@fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/000/SRR2176380/SRR2176380.fastq.gz /home/james/rnaseq/rawdata
ascp -l 100M -P 33001 -QT -k 2 -i /home/james/.aspera/connect/etc/asperaweb_id_dsa.openssh era-fasp@fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/001/SRR2176381/SRR2176381.fastq.gz /home/james/rnaseq/rawdata

数据下载后备份到一个文件夹

数据处理—— 简化名称

linux 重命名一个文件 mv test1.txt test2.txt

mv SRR2176358.fastq.gz BLO_S1_Rep1.fastq.gz
mv SRR2176359.fastq.gz BLO_S1_Rep2.fastq.gz
mv SRR2176360.fastq.gz BLO_S1_Rep3.fastq.gz
mv SRR2176361.fastq.gz KID_S1_Rep1.fastq.gz
mv SRR2176362.fastq.gz KID_S1_Rep2.fastq.gz
mv SRR2176363.fastq.gz KID_S1_Rep3.fastq.gz
mv SRR2176364.fastq.gz BLO_S2_Rep1.fastq.gz
mv SRR2176365.fastq.gz BLO_S2_Rep2.fastq.gz
mv SRR2176366.fastq.gz BLO_S2_Rep3.fastq.gz
mv SRR2176367.fastq.gz KID_S2_Rep1.fastq.gz
mv SRR2176368.fastq.gz KID_S2_Rep2.fastq.gz
mv SRR2176369.fastq.gz KID_S2_Rep3.fastq.gz
mv SRR2176370.fastq.gz BLO_S3_Rep1.fastq.gz
mv SRR2176371.fastq.gz BLO_S3_Rep2.fastq.gz
mv SRR2176372.fastq.gz BLO_S3_Rep3.fastq.gz
mv SRR2176373.fastq.gz KID_S3_Rep1.fastq.gz
mv SRR2176374.fastq.gz KID_S3_Rep2.fastq.gz
mv SRR2176375.fastq.gz KID_S3_Rep3.fastq.gz
mv SRR2176376.fastq.gz BLO_S4_Rep1.fastq.gz
mv SRR2176377.fastq.gz BLO_S4_Rep2.fastq.gz
mv SRR2176378.fastq.gz BLO_S4_Rep3.fastq.gz
mv SRR2176379.fastq.gz KID_S4_Rep1.fastq.gz
mv SRR2176380.fastq.gz KID_S4_Rep2.fastq.gz
mv SRR2176381.fastq.gz KID_S4_Rep3.fastq.gz

ls *.fastq.gz  > fastqc.lst

fastp -i BLO_S1_Rep1.fastq.gz -o BLO_S1_Rep1.gz -h BLO_S1_Rep1.html -j BLO_S1_Rep1.json

awk '{print "fastp -i "$1" -o cleandata/"$1" -h cleandata/"$1".html -j cleandata/"$1".json"}' fastqc.lst  > runfastp.sh

 sh runfastp.sh