https://gitee.com/lup9304/dapars/blob/master/Dapars_Installation.chm 师弟总结的指南,从上面链接可以直接下载。
DaPars:UnboundLocalError: local variable 'chrom_name' referenced before assignment报错 原始的输入文件 file.wig 如下所示: 1 3110982 3111121 4 1 3115138 3115146 1 1 3115146 3115149 2 1 3115149 3115152 3 1 3115152 3115161 4 在file.wig 文件中加上chr就可以解决报错了,如下所示: chr1 3110982 3111121...
DaPars is the first de novo tool that directly infers the dynamic alternative polyadenylation (APA) usage by comparing standard RNA-seq. Given the annotated gene model, DaPars can infer the de novo proximal APA sites as well as the long and short 3'UTR expression levels. Finally, the dynamic...
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DaPars——APA分析3’UTR Backgroud APA(alternative polyadenylation)在大多数人类基因的转录后调控中发挥着重要作用。通过使用不同的多聚腺苷酸化(poly(A))位点,基因可以缩短或延长含有顺式调控元件的3 'UTR,如microrna (miRNA)或RNA结合蛋白(RBP)结合位点3 ' UTR。因此,APA可以影响靶信使RNA的稳定性和翻译效率...
官网:https://github.com/3UTR/DaPars2 source activate dapars2 # 需要python2.7的环境! cd /data/APA_DaPars2 # 分析路径 step1 :这一步有两个文件需要从UCSC下载:whole_gene.bed, id_from_UCSC.txt。 1、下载:hg38_refseq_whole_gene.bed
DaPars的安装使用 http://lilab.research.bcm.edu/dldcc-web/lilab/zheng/DaPars_Documentation/html/DaPars.html http://www.zxzyl.com/archives/tag/apa https://www.nature.com/articles/ncomms6274 前几天表弟发给我dapars的东东,好像是生物学方面的一个算法之类的,而且这个算法还发过一篇nature文章,看能...
DaPars v2 is the next generation of DaPars that directly infers the dynamic alternative polyadenylation (APA) usage by comparing standard RNA-seq from multiple samples. Given the annotated gene model, DaPars v2 can infer the de novo proximal APA sites as well as the long and short 3’UTR ...
python /home/pc/biosoft/dapars/src/DaPars_Extract_Anno.py -b $refbed -s $genesymbol -o Dapars_extracted_3UTR.bed 遇到一个问题,困扰了好久,最后发现是genesymbol的问题,分隔符! 出错 解决后OK 和案例对比 下面寻找APA用的第一个方法: '/home/pc/biosoft/APAtrap/predictAPA' -i OHT1.sorted.bedgrap...
[--Fold-change-cutoff FOLD_CHANGE_CUTOFF] DaPars2(Modified): Dynamics analysis of Alternative PolyAdenylation from multiple RNA-seq data. optional arguments: -h, --help show this help message and exit base parameters: parameters used in DaPars2 base analysis -b gene_bed_file, --bed gene_bed...