Improve Research Reproducibility A Bio-protocol resource
Concise Method
tooltip

Conflict resolution

RL Ruijie Liu
WL Wai Yee Low
RT Rick Tearle
SK Sergey Koren
JG Jay Ghurye
AR Arang Rhie
AP Adam M. Phillippy
BR Benjamin D. Rosen
DB Derek M. Bickhart
TS Timothy P. L. Smith
SH Stefan Hiendleder
JW John L. Williams
request Request a Protocol
ask Ask a question
Favorite

The RH X chromosome marker order and orientation was generally in agreement with the X chromosome assembly. However, 15 out of 84 markers from the BovGen RH map and 18 out of 93 markers from the SUNbRH7000-rad map suggested a possible assembly error. Comparison of the RH maps showed that 5 markers from BovGen RH map and 4 markers from SUNbRH7000-rad map had a consistent arrangement that differed from the Brahman X assembly. Both RH maps showed an inversion of a 1,286,607 bp contig in a scaffold that is made up of 4 contigs. With the exception of this scaffold, other RH marker inconsistencies would have required contigs to be broken and rearranged. The Brahman X and ARS-UCD1.2 X agreed in all these regions so the order and orientation of scaffolds that agreed best with Hi-C and optical map was retained.

Outside of the PAR, the Y chromosome assembly is made up of small scaffolds with average length of 98,509 bp. The ordering of scaffolds was completely dependent on the 52 RH markers and no contig breaks were required.

Copyright and License information: The Author(s). ©2019
Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

Do you have any questions about this protocol?

Post your question to gather feedback from the community. We will also invite the authors of this article to respond.

0/150

tip Tips for asking effective questions

+ Description

Write a detailed description. Include all information that will help others answer your question including experimental processes, conditions, and relevant images.

post Post a Question
0 Q&A