使用conda进行安装conda install -c bioconda htseq=1.99.2 定量 HTSeq计算counts数有3种模式,如下图所示(ambiguous表示该read比对到多个gene上;no_feature表示read没有比对到gene上): htseq-count对链特异性及非链特异性数据的处理是不同的因此在处理数据前一定要明确目标数据的建库方式(链特异性或非链特异性的)...
PS:bioconda真心好用啊,但是好像不是所有的安装都是 conda install softname,好像有的软件需要其他的参数 记着就好啦,反正暂时没有遇到。
在基因层面的count计数的工具:Htseq-count,feature-count 1、Htseq-count 官网 https://htseq.readthedocs.io/en/release_0.11.1/count.html 它数count的模式 从它的第七种情况看出来:它没有办法解决基于转录本的定量,转录本存在可变剪接,这种overlap的情况很容易出现。 安装Htseq-count conda install htseq ht...
Install the dependencies with your favourite tool (pip,conda, etc.). To installHTSeqitself, run: python setup.py build install Testing To test locally, run ./test.sh To testhtseq-countalone, run it with the-ooption. A virtual environment is created in the.venvfolder andHTSeqis installed...
和featurecounts一样,htseq-count也是一款进行raw count定量的软件。该软件采用python语言进行开发,集成在HTseq这个包中。 对于python的包,通过pip可以方便的进行安装,代码如下 代码语言:javascript 复制 pip install HTSeq HTSeq提供了许多处理NGS数据的功能,htseq-count只是其中进行定量分析的一个模块。
configrna-seqjupyter-notebookcondapython3multiqctpmsalmonkallistofeaturecountspaired-endfastq-filescutadaptfastqchtseq-countsnakemake-workflow UpdatedOct 20, 2022 Jupyter Notebook Attempt at snakemake pipeline. Pyflow was forked fromhttps://github.com/crazyhottombut the Snakefile infrastructure and rule calli...
ubuntu安装kubernetesUbuntu安装conda 1. 下载安装包: https://www.anaconda.com/products/distribution#Downloads 通过 scp ~/Downloads/--- g8: ~/ 把下载在本地的安装包上传到服务器g8节点2. 在当前路径下,执行命 ubuntu安装kubernetes bash 下载安装 ...
cd../&&rm HTSeq-0.7.2-rf#或者conda install htseq HTseq统计Count的模式 共有3种,union, intersection_strict, intersection_nonempty 使用流程 htseq-count-f bam-r name-s no-a10\-t exon-i ID-m union.bam GFF \>count.txt#参数-f 输入格式bam/sam-r 对sam或者bam的排序方式。默认为name。HTse...
conda install htseq # 利用htseq-count对sort之后的bam文件进行reads计数 htseq-count-r pos-f bam/home/cenhui2018/QWJ/sequence_data/20191030_NGS_DATA/19R577_paired.hisat2_sorted.bam/home/cenhui2018/QWJ/sequence_data/genome/Anotation/gencode.vM23.annotation.gtf>19R577_paired.count2>/home/cenhu...
OSX in conda environments Apr 5, 2020 .travis_pypirc Starting work on deployment Jun 7, 2017 .travis_test.sh OSX in conda environments Apr 5, 2020 LICENSE No commit message Apr 7, 2010 MANIFEST.in MANIFEST.in includes more files