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Fix invocation of Picard programs in alignment and reference creation scripts

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@alecw alecw released this 15 Jul 14:56
· 50 commits to master since this release
v3.0.2
876b3b8

Changes

  • Fix invocation of Picard command-line programs in Drop-seq_alignment.sh and create_Drop-seq_reference_metadata.sh, which were broken by change to skinny picard.jar.
  • Reduce memory footprint of CorrectAndSplitScrnaReadPairs. Some metrics that were memory-intensive were removed.
  • Fix bug when processing reads that did not have UMI tag.
  • Upgrade to picard 3.1.1 to address security issue.
  • Add option GENE_SORT to CreateMetacells.
  • Enable multiple BAM input to FilterBAM.

Installation

Java

Download and unzip dropseq-3.0.2.zip . Wrapper scripts for all the command-line programs will be in the dropseq-3.0.2 directory that is created when unzipping.

R packages

Do this in the order below, because DropSeq.dropulation depends on DropSeq.utilities, and if you don't install that package first, the source version of DropSeq.utilities will be installed, which may be unstable.

install.packages("https://github.com/broadinstitute/Drop-seq/releases/download/v3.0.0/DropSeq.utilities_3.0.2.tar.gz") 
install.packages("https://github.com/broadinstitute/Drop-seq/releases/download/v3.0.0/DropSeq.dropulation_3.0.2.tar.gz")
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