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 htseq-count -h #查看是否安装成功 调用Htseq-count htseq...
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)...
在BAM文件,包含了比对上的reads和没有比对上的reads, 只有比对上的reads 会用来计数,htseq-count默认会根据mapping的质量值对BAM文件进行过滤,默认值为10, 意味着只有mapping quality > 10的reads才会用来计数,当然可以通过-a参数来修改这个阈值。 能够明确reads属于一个featurer时,比如示意图种的第一种情况,reads完...
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 ...
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...
用法:htseq-count [options] alignment_file gff_file alignment_file为比对得到的文件,通常为bam;gff_file为注释文件。 [options]中需要注意的有-f 指定alignment_file的格式,为bam或sam;-r指alignment_file按什么排序,有pos和name,需要根据bam文件设置;-s指链特异性,no指无特异性,yes指reads1是正义链, revers...
htseq-count [options] <alignment_file> <gtf_file> # 安装 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/...
Star121 master 8Branches 22Tags Code Folders and files Name Last commit message Last commit date Latest commit iosonofabio Update README.rst Apr 13, 2020 5ba0507·Apr 13, 2020 History 558 Commits example_data Tests for new htseq-count options ...
Install the dependencies with your favourite tool (pip,conda, etc.). To installHTSeqitself, run: python setup.py build install Documentation Please see: http://htseq.readthedocs.io Packages No packages published Languages C++54.5% Python43.6% ...