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How to Update the Restriction Digest File

(These instructions were necessary for the 2009 iteration of this course, but not for the 2011 course; I'm leaving them up here in case they do prove necessary, however.)

The Washington University Genome Sequencing Center has generated a new set of restriction digests (HindIII, SacI, EcoRI, EcoRV) for the D. grimshawi fosmids. The quality of this new set of restriction digests has improved compared to the original digests that were included in the finishing packages. You can use this new set of digests in conjunction with the original digests to verify your assembly. The new digest files are available here on gander. Once you navigate to the digest download page, please follow the following steps to view the new digests in Consed:

  1. Click on the link that corresponds to the name of your project.
  2. Right-click on the link "new_fragSizes.txt'" and choose "Download Link Target…".
  3. Copy the file to the edit_dir of your project directory in your virtual machine.
  4. Launch consed and click on the "Digests" button to configure the digest.
  5. Under "Full Pathname of Actual Gel Sizes File", change the name from "fragSizes.txt" to "new_fragSizes.txt".
  6. Update the fields under "What do you want to digest" and "Full Pathname of File of Vector Sequence" as usual.