search

sr-c / blog-comment

0 stars 0 forks source link

2018/10/02/local-nr-database/ #1

Open utterances-bot opened 4 years ago

utterances-bot commented 4 years ago

本地化nr数据库 - SR-C

数据库下载 nr数据库下载前应确认其序列ID中包含有gi信息。推荐通过NCBI提供的脚本进行下载。 1 perl update_blastdb.pl nr 下载完成后解压 1 tar -zxvf *.tar.gz 建库 由于下载的

https://sr-c.github.io/2018/10/02/local-nr-database/

XingyuLuo317 commented 4 years ago

-taxid_map gi_taxid_nucl.dmp这个参数是的文件是需要与nr的fasta数据放在同一目录下吗

sr-c commented 4 years ago

只需要通过-taxid_map参数传入gi_taxid_nucl.dmp的路径即可，不一定需要与fasta数据同目录。@lxy892987523

XingyuLuo317 commented 4 years ago

非常感谢您的快速回复，我想顺便请教一下，我在下载建好的nr数据库之后从nr.00 到 nr.38 全部放到 blast/db 之后直接使用nr数据库blastp的时候出现这样的no longer exists in database 有什么可能的原因吗，我是因为这样出现问题以后才查到您的博客打算重新用fasta格式的nr库重新建一个。我有确定我的环境路径设置正确了。

Sent from Mail for Windows 10

From: sr-c Sent: Thursday, August 6, 2020 9:25 PM To: sr-c/blog-comment Cc: lxy892987523; Mention Subject: Re: [sr-c/blog-comment] 2018/10/02/local-nr-database/ (#1)

只需要通过-taxid_map参数传入gi_taxid_nucl.dmp的路径即可，不一定需要与fasta数据同目录。@lxy892987523 — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.

-- This email has been checked for viruses by Avast antivirus software. https://www.avast.com/antivirus

sr-c commented 4 years ago

不知您的问题是否如此, 建议使用最新版本的BLAST+ 看是否能够解决。@lxy892987523

XingyuLuo317 commented 4 years ago

我就是只找到了这一篇跟我的情况差不多，但是也没有得到具体的结局办法，我用的是最新版的blast+，在windows下运行，后来为了确定是不是系统的问题，搭了一下WSL2的linux环境但是得到的结果是一样的。这里https://www.ncbi.nlm.nih.gov/books/NBK52637/是我参照的win下local blast搭建。

如果说下载库的时候没用官网的perl的script手动下载并解压会不会有影响。

Sent from Mail for Windows 10

From: sr-c Sent: Thursday, August 6, 2020 10:34 PM To: sr-c/blog-comment Cc: lxy892987523; Mention Subject: Re: [sr-c/blog-comment] 2018/10/02/local-nr-database/ (#1)

不知您的问题是否如此, 建议使用最新版本的BLAST+ 看是否能够解决。@lxy892987523 — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.

-- This email has been checked for viruses by Avast antivirus software. https://www.avast.com/antivirus

sr-c commented 4 years ago

建议使用官方脚本下载，保证数据库完整。@lxy892987523

XingyuLuo317 commented 4 years ago

好的，非常感谢您的耐心回复

Sent from Mail for Windows 10

From: sr-c Sent: Thursday, August 6, 2020 10:52 PM To: sr-c/blog-comment Cc: lxy892987523; Mention Subject: Re: [sr-c/blog-comment] 2018/10/02/local-nr-database/ (#1)

建议使用官方脚本下载，保证数据库完整。@lxy892987523 — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.

-- This email has been checked for viruses by Avast antivirus software. https://www.avast.com/antivirus

XingyuLuo317 commented 4 years ago

您好，我解决了那个数据库的问题了，没有用脚本下载的文件完整度没保证，重新下载以后解决了，同时我想问一下，把nr数据库与通过gi 关联到物种名的映射文件是应该选择 nucl还是prot，您的那篇博客里写的是nucl，我想确认一下。

Sent from Mail for Windows 10

From: sr-c Sent: Thursday, August 6, 2020 10:52 PM To: sr-c/blog-comment Cc: lxy892987523; Mention Subject: Re: [sr-c/blog-comment] 2018/10/02/local-nr-database/ (#1)

建议使用官方脚本下载，保证数据库完整。@lxy892987523 — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.

-- This email has been checked for viruses by Avast antivirus software. https://www.avast.com/antivirus