Skip to content

Dropulation + upgrade to picard 2.26.8, which includes log4j.16.0
Compare
Choose a tag to compare
@alecw alecw released this 17 Dec 00:44
· 227 commits to master since this release
v2.5.0
f85da7c

Picard and log4j upgrades

  • picard.jar v2.26.8, which includes log4j 2.16.0
  • remove stand-alone log4j.jar
  • upgrade to biojava 6.0.3
  • remove slf4j-log4j12

Dropulation programs - these programs are in support of our manuscript Natural variation in gene expression and Zika virus susceptibility revealed by villages of neural progenitor cells.

  • AssignCellsToSamples - This program takes as input a BAM file containing sequencing reads from a pool of donors, and a VCF file containing genotypes from those donors. The program emits the most likely donor for each cell.
  • DetectDoublets - This program takes as input a BAM file containing sequencing reads from a pool of donors, a VCF file containing genotypes from those donors, and the output from AssignCellsToSamples. The program emits the probability that each cell barcode is a doublet where a cell from two different donors have been co-encapsulated in the same droplet.

GTF parsing

  • pass command-line VALIDATION_STRINGENCY to GTFParser
  • Set default command-lin VALIDATION_STRINGENCY to LENIENT

Minor changes

  • improvements to sparse matrix I/O
  • allow merging of DGEs with same prefix if there are no cell barcode collisions.

See the Drop-seq alignment cookbook and Census-seq computational protocols for detailed usage instructions, diagrams, and explanations of how these new systems work. For more information about Census-seq, see our manuscript on bioRxiv

Assets 3
Loading