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@alecw alecw released this Apr 16, 2019 · 28 commits to master since this release

  • New program ConvertTagToReadGroup.
  • Encode quality tags as strings in TagBamWithReadSequenceExtended.
  • FilterBam bug fix: output file was not being close properly.
  • In DigitalExpression, allow null STRAND_STRATEGY and/or null LOCUS_FUNCTION_LIST, for BAMs that are not tagged with gene function.
  • In FilterBam and FilterBamByTag, add ability to output a summary file.

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

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@alecw alecw released this Apr 9, 2019 · 38 commits to master since this release

  • Support for SpermSeq

    • New program SpermSeqMarkDuplicates.
    • New program GenotypeSperm.
    • New program CreateSnpIntervalFromVcf.
    • See SPERMSEQ_COOKBOOK_LINK for details about how to use these and other Drop-seq programs to run SpermSeq analysis.
  • Add mutational pathway collapse strategy to CollapseTagWithContext. This collapse strategy looks at graphs of edit distance for collapse. All barcodes collapsed form a graph connected by nodes the given edit distance. For a cell barcode, find all sibling barcodes at up to some edit distance away, and collapse those barcodes into the core. Then find additional barcodes edit distance away from the children in the graph and collapse those in as well, up to some specified maximum edit distance.

  • New program ComputeUMISharing. If you collapse your barcodes (for example cell barcodes) in some fashion and tag your BAM with these new barocdes, this allows you to compute the UMI sharing between the original cell barcode and all of the barcodes that were collapsed into it. UMI sharing should be significantly high (>80% shared) if your collapse strategy was successful.

  • Handle gzipped TAG_VALUES_FILE in FilterBamByTag.

  • In TagBamWithReadSequenceExtended, added option to store barcode quality scores per base.

  • A number of bugfixes and argument checking to satisfy bug reports since the last release.

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

Assets 3

@alecw alecw released this Jan 15, 2019 · 75 commits to master since this release

  • Make GTF parsing more robust
  • Better error reporting of bad gene name in GTF
  • Sample alignment script bug fixes
  • In wrapper scripts, don't set TMPDIR environment variable to a directory that doesn't exist
  • CollapseTagWithContext adaptive edit distance now does a better job of selecting the proper edit distance threshold to use for a few rare edge cases
  • Respect TMPDIR environment variable in unit tests, and better unit test cleanup
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Pre-release

@alecw alecw released this Jan 15, 2019 · 76 commits to master since this release

This version of the software is not tagged in GitHub repository, because it predates this repository. Don't download this version unless you know what you are doing. It is obsolete.

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@alecw alecw released this Oct 11, 2018 · 95 commits to master since this release

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

@alecw alecw released this Sep 27, 2018 · 103 commits to master since this release

This is the version of Drop-seq tools that was available on http://mccarrolllab.org/dropseq/ prior to the creation of this GitHub repository.

Drop-seqAlignmentCookbookv1.2Jan2016.pdf

Note that the source code zip and tar.gz do not reflect the version of code used to build this release. The code used to build this release can be found in Drop-seq_tools-1.13.zip.

The version before this (1.12) can be found here

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