Diamond annotation versus Kallisto/Sleuth
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6.9 years ago
BioBing ▴ 150

Hi all Annotation Experts out there,

Currently, I am working with differential gene expression in a non-model organism. For this, I have used Kallisto/Sleuth and is very pleased with the process as well as the results.

But I am stuck and would be really grateful for some help to move on.

My issue is getting gene names into Sleuth instead of the Trinity "gene" names (for heat maps etc.). I have done an annotation of my de novo reference transcriptome (assembled with Trinity) in Diamond, which results in a .m8 file with accession numbers.

My questions are:

  1. how do I obtain gene names instead of accession numbers?
  2. how do I get my annotation with gene names into Sleuth? The examples I have seen is using ESEMBL and "pre-made" annotations from fx human/mice - how can I use my own annotation and get it into Sleuth?

Thanks in advance

Best wishes, Birgitte

RNA-Seq blast rna-seq R sequencing • 2.2k views
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Regarding you 2nd question, have a look at Trinotate and check this page on how to transfer Trinotate annotation to gene expression matrices. You may have yo modify the script to make it work for you

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Thank you! I am waiting for Trinotate to be configurated on the cluster I am using, that is why I have been using Diamond

Entering edit mode

Hi Birgitte, I'm now in the same situation as you more than a year ago...

I'm working with a non-model organism. I would like to use sleuth in R, but I don't know how to get my annotation with gene names into Sleuth.

Can you say me if you solved this?

Thank you!



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