Question: Diamond annotation versus Kallisto/Sleuth
1
gravatar for BioBing
3.5 years ago by
BioBing130
Denmark
BioBing130 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 • 1.4k views
ADD COMMENTlink modified 23 months ago by zx87549.7k • written 3.5 years ago by BioBing130
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 3.5 years ago by h.mon31k

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 3.5 years ago by BioBing130

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 23 months ago by lalvarez10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2035 users visited in the last hour