request Oar_rambouillet_v1.0ToOar_v3.1.over.chain.gz and Oar_v3.1ToOar_rambouillet_v1.0.over.chain.gz file
JJJAMBO
Dear UCSC Genome Browser database,
In order to make a better analysis in sheep, we selected the new highly contiguous sheep reference genome sequence (Oar_rambouillet_v1.0, GenBank assembly accession: GCA_002742125.1, https://www.ncbi.nlm.nih.gov/assembly/GCF_002742125.1/), and that of earlier draft genome sequence Oar_v3.1 is 40,376 bp). However, there is no available over.chain.gz file used for liftOver between new sheep reference genome (Oar_rambouillet_v1.0) and the earlier sheep reference genome ( Oar_v3.1). Therefore, I am writing to request you to provide Oar_rambouillet_v1.0ToOar_v3.1.over.chain.gz file which contains the liftOver data needed to convert Oar_rambouillet_v1.0 (sheep) coordinates to Oar_v3.1 (sheep). I would also like to request you to provide Oar_v3.1ToOar_rambouillet_v1.0.over.chain.gz file at the same time. I am sorry for any inconvenience I have caused. Thank you for your attention to these requests. I would like to thank you for your generous help in this case.
Yours sincerely,
Dr. Yuwei Gou
Gerardo Perez
Hello Dr. Yuwei Gou,
Thank you for your interest in the Genome Browser.
We have made an alignment of the oviAri3 assembly to the GCF_002742125.1 assembly hub. The two files are available on our download server:
GCF_002742125.1 → oviAri3: https://hgdownload.soe.ucsc.edu/hubs/GCF/002/742/125/GCF_002742125.1/liftOver/GCF_002742125.1ToOviAri3.over.chain.gz
oviAri3 → GCF_002742125.1: https://hgdownload.soe.ucsc.edu//goldenPath/oviAri3/vsGCF_002742125.1/oviAri3.GCF_002742125.1.all.chain.gz
The GCF_002742125.1 to oviAri3 Chain/Net tracks can be visualized here:
https://genome.ucsc.edu/h/GCF_002742125.1
I hope this is helpful. If you have any further questions, please reply 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
--
---
You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Public Support" group.
To unsubscribe from this group and stop receiving emails from it, send an email to genome+un...@soe.ucsc.edu.
To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/tencent_60684EB5933865DA08A16B560F32EB086E05%40qq.com.
Gerardo Perez
Hello Dr. Yuwei Gou,
My apologies. I sent the wrong oviAri3 → GCF_002742125.1 link in the previous email. The correct link should be the following:
oviAri3 → GCF_002742125.1: https://hgdownload.soe.ucsc.edu/goldenPath/oviAri3/liftOver/oviAri3ToGCF_002742125.1.over.chain.gz
We apologize for any inconvenience this may cause. If you have any further questions, please reply 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