gene expression RNAseq

Question

[domingues.pesca]

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

[jrt]

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).

[domingues.pesca]

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.

Answer 1

[GenoMax]

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.

Answer 2

[domingues.pesca]

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