首先从NCBI官网trace.ncbi.nlm.nih.gov/ 下载SRA软件 下面这条命令可以得到后缀为1和2的两个fastq文件 fastq-dump -I --split-files SRR390728 如果是直接下载了.sra文件,可以用如下命名得到paired end fastq文件 fastq-dump --split-files --split-3 SRR1813404.sra...
GATTACT+GTCTTAAC 1,当sampleSheet存在UMI(Unique Molecular indentifier,用于提高测序的准确性)时该项存在;为Read1的UMI序列+Read2的UMI序列信息,下图为文库中UMI的位置 1,1 表示 single read 2 表示 paired end N,是否过滤,Y表示被过滤,否则为N 0,偶数,没有控制位时为0 ATCCGA,index序列 第二行,Sequence ...
方法三:直接跑fastq-dump,用参数--split-files就自可以自动分辨出来,结果是一个文件就是single end,两个文件就是paired end。 方法四:fastq-dump的--split-spot可以用来分辨 srr="SRR3184279" numLines=$(fastq-dump -X 1 -Z --split-spot $srr | wc -l) if [ $numLines -eq 4 ] then echo "$srr...
I have downloaded SRR files (using prefetch). It says on the ncbi website that all of my runs have 2 reads per spot, but when I for example run SRR8743324 with: ./bin/fastq-dump --split-files SRR8743324, I only get one single fastq outpu...
fastq-dump -I --split-files SRR390728 Produces two fastq files (--split-files) containing ".1" and ".2" read suffices (-I) for paired-end data. --split-spot Split spots into individual reads. 一.SRA数据库: NCBI网站储存二代测序原始数据的数据库. ...
fastq-dump -I --split-files SRR390728 Produces two fastq files (--split-files) containing ".1" and ".2" read suffices (-I) for paired-end data. --split-spot Split spots into individual reads. 一.SRA数据库: NCBI网站储存二代测序原始数据的数据库. ...
fastp (single -end, SE) fastp -I SRR***.fastq -O SRR***_clean.fastq fastp (paired -end, PE) fastp -i Sample1-1_R1.fq.gz -o Sample1-1_R1.clean.fq.gz -I Sample1-1_R2.fq.gz -O Sample1-1_R2.clean.fq.gz fastp -i...
usage: fasterq_dump [-h] [-f FILE] [-k] [-t] [-w] [-m] [-u {all,curl,wget,prefetch}] [--log] [accessions [accessions ...]] A program to run fastq-dump sequentially on a list of accession numbers. Will automatically detect if reads are single- or paired-end and will run...
fastq-dump -I --split-files SRR390728 Produces two fastq files (--split-files) containing ".1" and ".2" read suffices (-I) for paired-end data. fastq-dump --split-files --fasta 60 SRR390728 Produces two (--split-files) fasta files (--fasta) with 60 bases per line ("60" in...
# * file cotains paired end data: output = prefix_1.fastq.gz, prefix_2.fastq.gz# * special case: unpaired reads in a paired end run end up in prefix.fastq.gz# * special case: if paired reads are stored in a single read, fastq-dump will split.# There might be a joining ...