Request for chain file generation: Drosophila melanogaster (dm6) and Rhodnius prolixus (RproC3)
María José Delgado
I'm a PhD student currently conducting comparative genomic analyses between Drosophila melanogaster and Rhodnius prolixus. To perform cross-species coordinate conversion (liftOver) and whole-genome alignments, I would like to kindly request your assistance in generating pairwise alignment chain files between the following two assemblies:
1. Drosophila melanogaster – dm6 / BDGP Release 6 (GCA_000001215.4)
2. Rhodnius prolixus – RproC3 / Rhodnius_prolixus-3.0.3 (GCA_000181055.3)
Available at NCBI: https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_000181055.3/
Also available through VectorBase (VEuPathDB): https://vectorbase.org/vectorbase/app/record/dataset/DS_4f4c90a272
Ideally, I would appreciate chain files in both directions (dm6 → RproC3 and RproC3 → dm6), however, even a single direction would be of great value for our analyses.
Please let me know if you need any additional information or if the Rhodnius prolixus assembly requires any specific format for processing.
Thank you very much for your time and consideration.
Best regards,
María José Delgado
Centro de Bioinvestigaciones - UNNOBA, Argentina
majo...@gmail.com
Gerardo Perez
Hello, María José.
Thank you for your interest in the Genome Browser.
We have made the requested liftOver chain files available on our download server:
dm6 -> GCA_000181055.3: https://hgdownload.soe.ucsc.edu/goldenPath/dm6/liftOver/dm6ToGCA_000181055.3.over.chain.gz
GCA_000181055.3 -> dm6: https://hgdownload.soe.ucsc.edu/hubs/GCA/000/181/055/GCA_000181055.3/liftOver/GCA_000181055.3ToDm6.over.chain.gz
I hope this is helpful. If you have any questions or need further assistance, please feel free to reach out to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
Gerardo Perez
UCSC Genomics Institute
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