conda install-c bioconda bowtie conda install-c bioconda bowtie2 conda install-c bioconda bwa 1.3 建立索引文件 参考:https://www.jianshu.com/p/89b35626befa 1.3.1 Hisat2 hisat2-build -p 2 Mycoplasma_hyorhinis_sk76.ASM31363v1.dna.toplevel.fa Mycoplasma_hyorhinis_sk76.ASM31363v1.dna.top...
1.软件安装 2 构建基因组索引文件 2.1 Hisat2 hisat2-build不支持基因组以压缩文件的形式输入,运行完成后,生成8个后缀名为ht2的文件。 使用帮助 2...
Hisat2和bowtie2比对后产生的Alignment summary的格式是一样的,如下: Alignment summary When HISAT2 finishes running, it prints messages summarizing what happened. These messages are printed to the "standard error" ("stderr") filehandle. For datasets consisting of unpaired reads, the summary might l...
Hisat2和bowtie2⽐对后产⽣的Alignment summary的格式是⼀样的，如下：Alignment summary When HISAT2 finishes running, it prints messages summarizing what happened. These messages are printed to the "standard error" ("stderr") filehandle. For datasets consisting of unpaired reads, the summary ...
「2. 一个转录组上游分析流程 | Hisat2-Stringtie」 「3.转录组无参比对教程 | Trinity」 写在前面 随着我们教程逐渐发布,我们转录组分析系列教程也逐渐分章节开放。若你有需要,可直接查看转录组上游分析教程[零基础(完)]。 个人笔记,可能会出现一些错误!
Test data to be used for automated testing with the nf-core pipelines - Added E. coli indexes for Bowtie2 HISAT2 and Bismark · nf-core/test-datasets@1626cfb
Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. 关于使用 使用它首先需要对参考基因组构建索引 【注意这里是基因组而不是参考转录组,因为它的BWA一样,是为基因组测序而生;如果是要比对参考转录组,那么就考虑hisat2吧】 ...
Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. 关于使用 使用它首先需要对参考基因组构建索引 【注意这里是基因组而不是参考转录组,因为它的BWA一样,是为基因组测序而生;如果是要比对参考转录组,那么就考虑hisat2吧】 ...
前面是用bowtie2比对的,换成hisat2就能找到了。总的来说,那个物种的基因组注释很不成熟,结果可能也不太可靠。【转发】@内含子:请教一个RNA-seq的问题:某个基因上有match,我在IGV上能看到,还不少,但经过st...
Inaddition to input and output, some modules will require index files and/or folders. Added E. coli indexes for Bowtie2 HISAT2 and Bismark 1626cfb Member ewels commented Mar 19, 2020 As these are tool specific, I guess they should be in the tool folder. Maybe tools/bismark/indices?