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Spatial meta-transcriptome analysis pipeline
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a subset of nt database for running SMTa #6

Open ZehangJiang opened 2 months ago

ZehangJiang commented 2 months ago

Hi there, when i use SMTa for microbe analysis in visium data, i noticed that the nt database is too large and time consuming. 114027 Can i just extract a subset (virus, bacterials and Fungi for human) of nt database from my downloaded file thus reduce time when running blastn? Thanks!

affinis commented 2 months ago

It's feasible to do that if you can subset the database, but how can you perform subset to indexed nt database files as you have shown in the picture? i don't known about any tools can do that

----- 原始邮件 ----- 发件人: "ZehangJiang" @.> 收件人: "affinis/SMTa" @.> 抄送: "Subscribed" @.***> 发送时间: 星期二, 2024年 6 月 25日 上午 11:45:04 主题: [affinis/SMTa] a subset of nt database for running SMTa (Issue #6)

Hi there, when i use SMTa for microbe analysis in visium data, i noticed that the nt database is too large and time consuming. 114027 Can i just extract a subset (virus, bacterials and Fungi for human) of nt database from my downloaded file thus reduce time when running blastn? Thanks!

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ZehangJiang commented 2 months ago

It's feasible to do that if you can subset the database, but how can you perform subset to indexed nt database files as you have shown in the picture? i don't known about any tools can do that … ----- 原始邮件 ----- 发件人: "ZehangJiang" @.> 收件人: "affinis/SMTa" @.> 抄送: "Subscribed" @.> 发送时间: 星期二, 2024年 6 月 25日 上午 11:45:04 主题: [affinis/SMTa] a subset of nt database for running SMTa (Issue #6) Hi there, when i use SMTa for microbe analysis in visium data, i noticed that the nt database is too large and time consuming. 114027 Can i just extract a subset (virus, bacterials and Fungi for human) of nt database from my downloaded file thus reduce time when running blastn? Thanks! -- Reply to this email directly or view it on GitHub: #6 You are receiving this because you are subscribed to this thread. Message ID: @.>

Sorry, the above picture is for showing the size of nt database (709G). I also wondering how i can subset a human source microbiome nt library from the total library...

affinis commented 2 months ago

a possible way is to download Virus/bacteria/fungi database independently from NCBI, but that can not guarantee 'human source', in addition, the pipline needs taxids in the database, and taxids are included in complete nt database by default, if you download another one, taxids may not be included in it by default.

----- 原始邮件 ----- 发件人: "ZehangJiang" @.> 收件人: "affinis/SMTa" @.> 抄送: "affinis" @.>, "Comment" @.> 发送时间: 星期二, 2024年 6 月 25日 下午 1:08:17 主题: Re: [affinis/SMTa] a subset of nt database for running SMTa (Issue #6)

It's feasible to do that if you can subset the database, but how can you perform subset to indexed nt database files as you have shown in the picture? i don't known about any tools can do that … ----- 原始邮件 ----- 发件人: "ZehangJiang" @.> 收件人: "affinis/SMTa" @.> 抄送: "Subscribed" @.> 发送时间: 星期二, 2024年 6 月 25日 上午 11:45:04 主题: [affinis/SMTa] a subset of nt database for running SMTa (Issue #6) Hi there, when i use SMTa for microbe analysis in visium data, i noticed that the nt database is too large and time consuming. 114027 Can i just extract a subset (virus, bacterials and Fungi for human) of nt database from my downloaded file thus reduce time when running blastn? Thanks! -- Reply to this email directly or view it on GitHub: #6 You are receiving this because you are subscribed to this thread. Message ID: @.>

Sorry, the above picture is for showing the size of nt database (709G). I also wondering how i can subset a human source microbiome nt library from the total library...

-- Reply to this email directly or view it on GitHub: https://github.com/affinis/SMTa/issues/6#issuecomment-2187988842 You are receiving this because you commented.

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