一个很有趣的工具-TCGA2BED-可以从TCGA数据库提取数据成bed格式

Jimmy

bed格式我就不多说了，大家的老朋友了，而且有一个bedtools，号称要替代生信工程师，呵呵~~~
看这个图就明白了，非常赞~~~


这个工具发表在：http://bmcbioinformatics.biomedc ... 6/s12859-016-1419-5
主要有3个功能，最后还可以把TCGA数据库抓取的内容，整合上 UCSC, HGNC, NCBI Entrez Gene, and miRBase 的内容。
We created and are maintaining an open access FTP repository (ftp://bioinf.iasi.cnr.it/), which contains the original TCGA data sets  addressed by TCGA2BED and the corresponding data converted into the BED format.
这个FTP很赞，很赞！！！
那么TCGA有什么数据呢，我就不翻译了：
TCGA includes several Next Generation Sequencing (NGS) experimental data types, i.e., Copy Number Variation (CNV) , DNA-methylation , DNA-sequencing (DNA-seq)  including whole genome and whole exome mutations, Gene expression (RNA-seq V1, RNA-seq V2) , microRNA sequencing (miRNA-seq) , and their meta data (clinical and biospecimen information) , which are organized into three levels

ant

这个 open access FTP repository (ftp://bioinf.iasi.cnr.it/)现在连不上，你们可以吗？