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
2 answers
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.
Thank you very much for all tips. I just solved it using https://gitlab.com/fethalen/bfg.
Log in to answer this question.
-
How to find orthologus sequences between the different species of non-model organisms?
written by sunnykevin97
-
what should I do first: transciptome annotation or DE analysis?
written by vinicius •
-
Can you detect novel (non-coding) transcripts using Salmon and the hg38 transcriptome?
written by c_u
-
How to calculate TPM of transcripts with isoforms
written by marcosp.belem •
-
Help in Trinity
written by kartikayprasad •
-
Method to identify novel transcript based on strand-specific RNAseq
written by biolab
-
DGE using trinity
written by loly.pearl86 •
-
having up-regulated and down-regulated isoforms in Trinity output
written by Whoknows
-
merged transcripts from RNA de novo assembly to create a reference transcriptome
written by teixe005 •
-
How To Compare 2 Differential Expressed Transcripts From 2 Different De Novo Assembly?
written by nbvasani
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).
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.