what database did you select?
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How to batch download multiple mitochondrial FASTA & GFF files?
Downloading 1 by 1 is taking an eternity.
I have a refseq_mito.txt file with 115 RefSeq accession numbers for mitochondrial genomes (examples below)
refseq_mito.txt contents example:
NC_019663.1
NC_023340.1
NC_019642.1
NC_005291.1
NC_023371.1
I've tried to input this refseq_mito.txt into Batch Entrez (Database: Genome) which sends me to this page:
which sends me to a page showing 10 tick genome NOT mitochondria:
What am I doing wrong? How can I get FASTA & GFF of the mitochondria I'm interested in?
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When I tried your example ID's it got me the correct results. Once that works downloading the data should follow Send to -> File -> Format -> GFF3 and Send to -> File -> Format -> FASTA. You will get a single file with sequence/GFF data for all organisms. You will need to split them into individual files.
This is where I was going wrong, I've been trying "Genome" and "Assembly". Many thanks for helping with this!
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Have you tried clicking the link that says "Retrieve records for 110 UIDs"? That is what you probably want.
GFF files for mitochondrial genomes are not directly available. You have to select a genome e.g. https://www.ncbi.nlm.nih.gov/nuccore/NC_011943.1 and then click on Send to -> File -> Format -> GFF3
The "Retrieve records for 110 UIDs" just sends me to the 10 tick genomes page (Shown above, second picture) with no mention of mitochondria.
I can individually click on the mitochondrial genomes to manually download both FASTA and GFF but this will be time consuming for over 100 mitochondrial genomes.
Can you post a few example accession numbers?
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