Running kallisto

Written by bonohu in rnaseq on 月 22 1月 2018.

If a transcriptome sequence set is available for the organism, kallisto can be used for transcript quantification. The kallisto version I used was 0.43.1, which was previously installed using Homebrew by the command like brew install kallisto.

kallisto index -i index transcriptome.fa
kallisto quant -i index -o …

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Why blog in English

Written by bonohu in misc on 土 20 1月 2018.

I have continuously updated my blog in Japanese which was hosted in my server at home. The server was broken early this month, and I thought how to resume that.

I published a book for biological data analysis in Japanese which was a clean summary of my blog in Japanese …

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Written by bonohu in DBCLS on 木 18 1月 2018.


Joined SPARQLthon for Jan 2018 was held at DBCLS Kashiwa. This was 64th SPARQLthon.

I will hack for the development of AOE, index of public omics (gene expression) data.


Tackling to hack parsers for inputing metadata from NCBI GEO utilizing DBCLS SRA API. Thanks to this API, we …

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