Schmidtea mediterranea annotation problems
I am doing RNA-Seq analysis of Schmidtea mediterranea(fresh water planaria). The major problem is annotation. How do I get any useful gene data from the up and down regulated hits that I got (or just assuming I have a subset of "mkids"). I used annotation files from the Smed database which has only gene predictions(from maker) and the annotation from wormbase has only "mk" ids . I have used genomes from worm base and SmedDB.Also how can I get GO enrcihment and pathway enrichment for the hit genes(mkids or maker gene predictions)?
• 1,482 views
•
link
written
by
kalmeshv83 •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
How to compare and complement the missing gene and feature in gff3 file base on available gff3 refe…
written by Sony Nguyen •
-
Adding functional annotation and meta-data of MAKER/BRAKER GFF
written by javanokendo •
-
Interpreting first round of maker
written by gilsorek12 •
-
How to get proteins from GFF file resulted from MAKER annotation
written by imda •
-
Functional Annotation with Maker
written by RBGE-Hillebrandia •
-
Annotation pipelines in 2018
written by Ric
-
MAKER AED score
written by Tye Kahn •
-
Incorporate new genes info to the reference gff file for running stringtie or equivalent program
written by bioinfo17 •
-
Selecting primary transcript for each locus from a GFF file
written by arnstrm
-
Maker Obtain A Consensus Model
written by larriba.ed •
You could obtain GO-terms by blasting against UniProt and using hmmer against Pfam. Maybe eggnog (http://eggnogdb.embl.de/#/app/home) could be of use?
Thanks. Do you know how i can get the actual genes from the maker gene predictions?I know I can get the gene sequence and then blast it and know the gene but how do I do it for all genes at once?