GTF file for Rhinolophus sinicus

Question

[ara]

Hello,

I am currently working on a project investigating tissue-specific alternative splicing in Rhinolophus sinicus, particularly focusing on cochlear adaptations during seasonal transitions. I am in need of a GTF (Gene Transfer Format) file for this species to aid in my RNA-sequencing analysis. Could anyone kindly direct me to where I can find the relevant GTF file for Rhinolophus sinicus, or recommend databases that might have the necessary information?

Answer 1

[GenoMax]

Visit the genome page of this organism at NCBI here --> https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_001888835.1/ . Click on Download button. That will open a dialog box. You should be able to download genome sequence (get the RefSeq version) and GFF/GTF files from that page. Make sure you use matched files obtained from this page.

Edit: In late April 2024 the page linked above carried a warning from NCBI that said that this genome was contaminated. While the downloads seem to work, you would be using the data at your own risk.

If the status changes in future this edit will be removed.

[atowns21]

This download doesn't seem to work for me. There is a message on the website saying "Warning: contaminated. Status: RefSeq GCF_001888835.1 is suppressed". Is there any other way to download the genome for rhinolophus sinicus (gtf/fa files)?

[GenoMax]

I was able to get the GTF file. I tried the fasta genome and it seemed to work but I did not complete the download. If you choose to ignore the warning on the NCBI page you will use the data at your own risk. This assembly appears to be contaminated.

[atowns21]

Ah gotcha. I guess what doesn't make sense to me is why a paper published in 2022 uses that reference genome.