Hi everyone,
I used HTSeq-count to count mapped reads to genes giving in input the bam file get from STAR and the gff annotation file downloaded from NCBI (used also for indexing the genome, also downloaded from NCBI).
I want to find differentially expressed genes in different species of Drosophila. The problem is that these species have gene symbols like LOCXXXXXXXXX where X are numbers. E.g. Using NCBI Blast, LOC108015140 in D. suzukii corresponds to Zw in D. melanogaster.
Is there a way to "translate" these gene symbols into the D. melanogaster one?
WIthout knowing how these genomes were annotated its difficult to know. Indeed the answer may come down to doing your own orthology analysis.
Flybase has a list of orthology relationships for the species that it covers, which you can download here: ftp://ftp.flybase.net/releases/FB2019_03/precomputed_files/orthologs/dmel_orthologs_in_drosophila_species_fb_2019_03.tsv.gz
but that is only for its species it covers, which, for example doesn't include D. biamipes.
Thank you for answering. Unluckely Flybase also uses different orthologs gene symbols with respect to the NCBI.
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That gene location is actually from
Drosophila suzuki(https://www.ncbi.nlm.nih.gov/gene/108015140 ).Yes, sorry, I edit the post.