ucsc数据库怎么使用(ucsc数据库使用方法)

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大家好，今天来介绍ucsc数据库怎么使用的问题，以下是渲大师小编对此问题的归纳和整理，感兴趣的来一起看看吧！

ucsc xena数据库如何做KaplanMeier 。

首先打开地址，然后输入基因敬历，点击生成图片。
Kaplan-Meier数据库的来源包括GEO，EGA和TCGA。
该工具的主要目的是基基稿者于荟萃分析的生存生物搏薯标记物的发现和验证。

如何从UCSCGenomeBrowser中单独或批量获取gene中的各类序列

利用UCSC的Table
Browser页面可以非常简单的单独或批量获取gene中稿春氏的各类序列，使用方法：
goto
http://genome.ucsc.edu/
点击页面上方的Tables，选择你需键散要的organism
and
assembly，
如果想到refseq
UTRs序列，选择"Genes
and
gene
predictions
tracks"
"Refseq
Genes"
"refGene"
region
is
set
to
"genome"
identifiers
中可以填入你需要的gene列表
output
format
to
"sequence"
可以写入文件名，下载文件
click
"get
output"
chose
"genomic"
chose
"3'
UTR
Exons"
还可以定义输出序森侍列的大小写等。

如何用ucsc画bigwig图

Because the bigWig files are indexed binary files, they can be difficult to extract data from. Consequently, we have developed the following two programs, both of which are available from the directory of binary utilities.

bigWigToBedGraph — this program converts a bigWig file to ASCII bedGraph format.
bigWigToWig — this program converts a bigWig file to wig format.
bigWigSummary — this program extracts summary information from a bigWig file.
bigWigInfo — this program prints out information about a bigWig file.

from http://genome.ucsc.edu/goldenPath/help/bigWig.html

1、从http://hgdownload.cse.ucsc.edu/admin/exe/ 选择相应系统的软件库目录，从目录下下载相应的二进制文件

2、利用 chmod 0755 或 chmod a+x 修改文件权限使得文件可执行

3、在当前目录下运行
./bigWigToWig

出现问题： ./bigWigToWig: error while loading shared libraries: libssl.so.10: cannot open shared object file: No such file or directory
原因：系统的libssl.so.1.0.0文件不能找到
解决问题：在系统中查找该文件，如有携孝，建立连接 使得能够找到该库文件，如果没有下载
sudo ln /lib/x86_64-linux-gnu/libssl.so.1.0.0 /usr/lib/libssl.so.10

4、再次在当前目录下运行
./bigWigToWig

出现问题：./bigWigToWig: error while loading shared libraries: libcrypto.so.10: cannot open shared object file: No such file or directory
原因：系统的libcrypto.so.10文件不能找到
解决问题：在系统中查找该文件，如有，建立连接 使得辩粗稿能够找到该库文件，如果没有下载
sudo ln /lib/x86_64-linux-gnu/libcrypto.so.1.0.0 /usr/lib/libcrypto.so.10

5、再次在当前目录下运行，成功，显示软凳则件的使用介绍
./bigWigToWig

bigWigToWig - Convert bigWig to wig. This will keep more of the same structure of the
original wig than bigWigToBedGraph does, but still will break up large stepped sections
into smaller ones.
usage:
bigWigToWig in.bigWig out.wig
options:
-chrom=chr1 - if set restrict output to given chromosome
-start=N - if set, restrict output to only that over start
-end=N - if set, restict output to only that under end
-udcDir=/dir/to/cache - place to put cache for remote bigBed/bigWigs

番茄数据库如何找染色体长度

在UCSC的主页上，点击Genomics，然后点击human图标，获取其他物种的染色体长判茄度。如闷
染色体（chromosome）是细胞在有丝分裂或减数分裂时掘橡察DNA存在的特定形式。细胞核内，DNA紧密卷绕在称为组蛋白的蛋白质周围并被包装成一个线状结构。当细胞不分裂时，染色体在细胞核中是不可见的——在显微镜下也是如此。

如何从UCSC数据库中得到GTF注释文件

For tRNA/rRNA:
* Select "All Tables" from the group drop-down list
* Select the "rmsk" table from the table drop-down list
* Choose "GTF" as the output format
* Type a filename (e.g. "rRNA.tRNA.gtf"枯雀数) in "output file" so your browser downloads the
result
* Click "create" next to filter
* Next to "repClass," type rRNA
* Next to free-form query, select "OR" and type repClass = "tRNA"
* Click submit on that page, then get output on the main page

For chrM genes:

* Select "All Tables" from the group drop-down list
* Select the "knownGene" table from the table drop-down list
* Choose "没首岁碧GTF" as the output format
* Type a filename (e.g. "chrM.gtf") in "output file" so your browser downloads the result
* Click "create" next to filter
* Next to "chrom," type chrM
* Click submit on that page, then get output on the main page