Skip to content

First release based on open-source code

Choose a tag to compare

View all tags
@alecw alecw released this 11 Oct 13:01
v2.0.0
1ef3a59
This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
GPG key ID: 4AEE18F83AFDEB23
Expired
Verified
Learn about vigilant mode.

There are a number of enhancements to the Drop-seq platform that come with version 2.0.0:

  1. New methods to clean up the cell barcodes from bead synthesis errors and PCR errors result in less clutter in the data when trying to decide which cell barcodes are truly cells.
  2. Enhanced Digital expression to be more flexible in how it interprets gene annotations, allowing the program to extract both intronic DGE data as well as the typical coding+utr data.
  3. New reference meta data tools and a shell script to generate reference meta data.
  4. Slightly less arbitrary program names and argument names, with a consistent set of rules so future programs don't run into the same problems.
  5. Bug fixes (!)

Please note that command line argument format will soon be changing slightly. This is due to Picard (which we build on top of) changing in the future: Below is an example command line showing the difference between the old and new syntax, with the old command line shown first:

java -jar build/libs/picard.jar SortSam I=testdata/picard/sam/namesorted.test.sam SORT_ORDER=coordinate O=sorted.sam

java -jar build/libs/picard.jar SortSam -I testdata/picard/sam/namesorted.test.sam -SORT_ORDER coordinate -O sorted.sam

See the Drop-seq alignment cookbook for detailed usage instructions, diagrams, and explanations of how these new systems work.

Assets 3
Loading