Gene name ?

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lg2...@gmail.com

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Oct 1, 2019, 11:29:24 PM10/1/19

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Dear Authors,

Just started using the software today and what an entry way to RNA-seq analysis !!

I was already using Kallisto for mapping and tximport for creating the table. But in doing so, I was getting the gene names (not id).

I understand that here we also have the data transcripts to look at splicing etc... but would it be possible to get an extra column with the gene name ??

That would greatly help. Don't know if it's achievable?

Also, how much "cleaning" of low expressing genes is too much ?

Thanks for your help and congrats on such a great piece of software

Laurent

wenbin guo

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Oct 2, 2019, 6:06:42 AM10/2/19

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Dear Laurent,

Many thanks for using our App.

One of the input files for 3D analysis is the transcript-gene association csv table. In this table, the first column must be the transcript names that match to the Kallisto quantification. The second column is the genes which the transcripts belong to. This gene column can be any format. It is just a "name" of the gene. you can use gene id, e.g. AT1G01060; you can use gene name, e.g. LHY, or you can even use fictional name, e.g. AT1G01060_LHY, gene1, this_is_gene1, etc.