I downloaded 100s of gene orthologs from ENSEMBL using FASTA format. I have headers that look a lot like this one:
>EMLSAP00000005133
or this one:
>ENN75927
I would like my headers to have the following format:
>Scientific_name_geneName_EnsemblID
Based on my research, I've seen that using the prefixes from the ensembl IDs, I should be able to find the scientific names. I have also seen that I could use BiomaRt in order to find the gene name. However, I am having trouble using BiomaRt in the command line and being able to automatically transform the hundreds of headers from the different files.
Could someone help me? Is there a way of doing all of this (scientific name and gene name) in the same step or is this approach the correct one?
•
written
by
Nata Ali •
0 answers
No answers yet.
Log in to answer this question.
-
Sheep-Human ortholog mapping with BioMart and Orthogene/Gprofiler
written by Michael •
-
How to assign gene names to ensembl IDs if species not in Biomart
written by bioinfo •
-
Ensembl ID mapping using Biomart
written by prithvi.mastermind •
-
Is there a way to batch convert a list of Bacterial Ensembl accessions to a list of gene locations?
written by biobaker •
-
biomaRt getBM function report some NA
written by Bastien Hervé
-
Correct formatting for IDs in OMA standalone .splice files to properly identify splice variants
written by eschang1 •
-
How to retrieve Gene name from SNP ID using biomaRt
written by johnS •
-
BioMart up-to-date with NCBI ?
written by lindfors.erno •
-
Biomart Annotation
written by int11ap1
-
Mapping Snps To Genes (And Pathways, Go, Etc.)
written by Stephen
