Question: gene expression RNAseq
0
gravatar for domingues.pesca
17 months ago by
domingues.pesca0 wrote:

Hi all I am new in bioinformatics and need some help. I did a DEG analysis from Trinity transcripts using a de novo reference. First I did a count table using Salmon, then I did DEG analysis using edgeR. Now I would like to annotate the transcripts differently expressed, but I do not how I can to do that. I just tried to get my transcripts differently expressed sequence from fasta file using a ID list, but I can't to do that using grep command (it didn't work). Does someone any idea?

I will appreciate any answer.

Thanks

deg rna-seq • 424 views
ADD COMMENTlink modified 17 months ago • written 17 months ago by domingues.pesca0

annotate the transcripts differently expressed, but I do not how I can to do that.

Need more detail here. What type of annotation are you interested in? gene symbols, chr positions, sequence information, GO classification, pathway memberships,...

If you are working in R, the biomaRt package gives you access to a wide array of gene/protein annotations from Ensembl. The annotables package (https://github.com/stephenturner/annotables) is a nice example using biomaRt to retrieve some basic gene annotations (gene symbols, description, chr position, etc).

org.Hs.eg.db is an Entrez-based annotation R package for human (with similar packages for other species).

ADD REPLYlink modified 17 months ago by ATpoint46k • written 17 months ago by jrt0

Hi

My RNAseq are of a shark (Isurus oxyrinchus). I would like to do GO classification and KEGG pathway of DEG. But my main concern here is how I could to get fasta sequences from a ID list. Although it seems easy I saw many post about that but it was unsuccessful for me using grep command.

ADD REPLYlink written 17 months ago by domingues.pesca0
0
gravatar for GenoMax
17 months ago by
GenoMax96k
United States
GenoMax96k wrote:

To get the sequences using an ID list the best option is to use a utility called faSomeRecords from Jim Kent (UCSC). Here is a link for more information: A: Extract Sequence From Fasta File Using Ids From a separate txt File in linux

You will want to use TransDecoder to identify coding regions in your sequences before doing annotation.

ADD COMMENTlink modified 17 months ago • written 17 months ago by GenoMax96k
0
gravatar for domingues.pesca
17 months ago by
domingues.pesca0 wrote:

Thank you very much for all tips. I just solved it using https://gitlab.com/fethalen/bfg.

ADD COMMENTlink written 17 months ago by domingues.pesca0
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