bowtie2 -p 10 -x genome_index -1 input_1.fq -2 input_2.fq | samtools sort -O bam -@ 10 -o - > output.bam 需要注意的是: 这条命令把bowtie2 生成的sam文件通过管道|传递到samtools,将sam转换为bam文件,省去中间sam文件的空间占用 genome_index 指的是用于bowtie2的索引文件(如下图),而...
# 使用参考序列构建索引,index为索引前缀 bowtie2-build lambda_virus.fa index # 目标序列与参考数据库进行比对 # 对双端序列比对 bowtie2 -x index -1 reads_1.fq -2 reads_2.fq -p 32 -S example_pair.sam # 对单端序列比对 bowtie2 -x index -U reads_1.fq -p 32 -S example_single.sam ...
genome_index 需要指定路径及其共用文件名,比如我的索引文件放在/data/ref/bowtie2/mm10目录下,但是需要输入的参数为/data/ref/bowtie2/mm10/mm10。最后一个mm10指的是共用文件名。 必需参数 可选参数(常用) 使用(构建索引) 官方索引 wget ftp://ftp.ccb.jhu.edu/pub/data/bowtie2_indexes/mm10.zip ...
摘要:[Bowtie和Bowtie2使用]bowtie 比对http: bowtie-bio sourceforge net index shtmlhttp: www ncrna net bowtie-short-sequence-alignment-tool-detailed-solution http: www plob org 2011 12 13 932 html 常见的短序列比对工具有很多,如fasta、blast、bowtie、shrimp、s…… [关键词:碱基 序列 种子 前导...
Change max size of small index to 2GB when using SAIS Jan 4, 2024 bowtie2-inspect Update python scripts to support python3 Jan 8, 2020 bowtie_build_main.cpp Changing my email address Dec 19, 2012 bowtie_main.cpp merging in master ...
Build a set of index files for the Drosophila genome. An error message appears if you do not have the Bowtie 2 Support Package for Bioinformatics Toolbox installed when you run the function. Click the provided link to download the package from the Add-on menu. For this example, the refere...
bowtie2 -x lambda_virus -U /home/pxy7896/Downloads/bowtie2/example/reads/reads_1.fq -S eg1.sam 参数解释: -x:查看index文件首先在当前目录下找,找不到再去环境变量BOWTIE2_INDEXES下找。 -U:后面跟需要比对的read文件。多个用,分隔。
No index, query, or output file specified! There is no mention of bowtie2 being a dependency in the documentation as far as I can see, only bowtie1 is listed. Which version is actually supported? brianjohnhaas commentedon Oct 17, 2016 ...
Click the provided link to download the package from the Add-on menu. For this example, the reference sequence Dmel_chr4.fa is already provided with the toolbox. status = bowtie2build('Dmel_chr4.fa', 'Dmel_chr4_index'); If the index build is successful, the function returns 0 and ...
genome_index 需要指定路径及其共用文件名,比如我的索引文件放在/data/ref/bowtie2/mm10目录下,但是需要输入的参数为/data/ref/bowtie2/mm10/mm10。最后一个mm10指的是共用文件名。 必需参数 可选参数(常用) ...