MAINTENANCE OUTAGE: The University Wiki Service will undergo maintenance on September 26th, 2017, from 6 pm to 8 pm. During this 2 hour time period https://wikis.utexas.edu may be unavailable. Users are advised to save content locally that may be needed during this time and to otherwise save all edits as unsaved work may be lost. Please contact the UT Service Desk at 512-475-9400 for any questions.
The University Wiki Service has upgraded the Confluence Server software, from version 5.9.14 to 5.10.8. Please refer to the knowledge base article, KB0015891, for a high level summary of upgrade changes. Thank you!
Skip to end of metadata
Go to start of metadata

Note: Compatibility issues with Maq 0.7.1 and Maqview 0.2.3 have been experienced. So, use Maq 0.6.6 and maqview 0.2.3 together.

With a reference file ref.bfa and an maq alignment file out.map :

maq assemble -s out.cns ref.bfa out.map

maqindex -i -c out.cns out.map chr1   (here chr1 is just a header of one of the sequences in the ref.bfa file)

maqview -c out.cns out.map  (needs X terminal to work)

  • No labels