Question: Diamond annotation versus Kallisto/Sleuth
1
gravatar for BioBing
20 months ago by
BioBing100
Denmark
BioBing100 wrote:

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

sequencing blast rna-seq R • 760 views
ADD COMMENTlink modified 28 days ago by zx87546.1k • written 20 months ago by BioBing100
1

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

ADD REPLYlink written 20 months ago by h.mon21k

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

ADD REPLYlink written 19 months ago by BioBing100

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!

LucĂ­a

ADD REPLYlink written 29 days ago by lalvarez10
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