Question: Diamond annotation versus Kallisto/Sleuth
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gravatar for BioBing
4 weeks ago by
BioBing50
Denmark
BioBing50 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 • 128 views
ADD COMMENTlink written 4 weeks ago by BioBing50
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 4 weeks ago by h.mon5.7k

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 28 days ago by BioBing50
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