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CHANGELOG.rst

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Changelog

[Unreleased]

Changed

  • Gene sequence poly-A tail in Split-seq protocol is now trimmed
  • Fixed processing of GTF files without tags
  • Fixed bug with no permission to write temporary files in dropReport

[0.8.6] - 2019-08-01

Added

  • Protocol aliases for Drop-seq, Seq-well and CEL-Seq2

[0.8.5] - 2018-11-14

Changed

  • Compatibility with preseqR-4.0.0
  • Compatibility with newer boost versions
  • Fixed "merge-umi" cli option in dropest
  • More informative dropEst logging
  • Fixed bug with false warning on "Unexpected chromosome -1"
  • Fixed bug with wrong work of "-F" option with "-u" #### Added
  • dropTag now able to trim and filter gene reads based on quality (see TagsSearch/Processing section of "configs/config_desc.xml")
  • Pipeline can be installed with make install now
  • Support for SPLiT-seq protocol (DOI: 10.1126/science.aam8999)

[0.8.3] - 2018-05-17

Changed

  • Fixed bug with merge failure without barcode file
  • Fixed bug with -C and -u options
  • Fixed logs for bam output
  • Fixed output of reads_per_umi_per_cell
  • Barcodes for 10x chromium v2.0

[0.8.2] - 2018-04-20

Changed

  • Config field "Estimation/Merge/barcodes_file" now accepts paths, relative to config directory, as well as path with "~/"
  • Fixed bug which perevented passing several files to -r option of dropest (Issue #25)
  • Fixed bug with wrong bam output (-F option)
  • Bam output now saves info about raw barcode sequences, read type and barcode quality similarly to 10x CellRanger format
  • Updated dockers for CentOS 6 and Cent OS 7
  • Fixed bug, when UMIs with N nucleotides weren't removed
  • Fixed bug with incorrect processing of read type tag, when it has type "A" (Issue #18)
  • Pipeline now uses information from gene bam tag for intergenic reads when provided #### Added
  • To improve reproducibility, config file is now copied to the log directory
  • 'Directional' UMI correction can be applied during dropEst phase with "-u" option. In this case, information for more advanced UMI correction isn't saved to the output rds.

[0.8.1] - 2018-04-06

Changed

  • Fixed some bugs in dropestr #### Added
  • Added protocol type 10x (which is alias for indrop3) to dropTag

[0.8.0] - 2018-03-20

Changed

  • Now, information about reads is kept in separate file instead (*.reads.gz), which should be passed to dropEst
  • New format of reads_per_umi_per_cell in cell.counts.rds

Added

  • UMI correction algorithm now uses UMI quality (only Illumina 1.8 or later formats are supported)

[0.7.6] - 2018-02-22

Added

  • Version number output in dropEst #### Changed
  • Fixed bug with report generation
  • Fixed bugs with estimation of low-quality cells

[0.7.5] - 2018-01-28

Added

  • Dockers for Centos6, Centos7 and Debian9
  • iclip protocol support
  • 10x barcodes
  • Published code for filtration of multialigned reads from bam files with cell mixture. #### Changed
  • Optimized precise merge performance
  • Fixed bug with fastq split during dropTag
  • New format of barcode files
  • Optimized memory usage in parsing read params from file
  • Algorithm of filtration of low-quality cells was significantly improved

[0.7.1] - 2017-10-18

Added

  • Integration with velocyto

[0.7.0] - 2017-10-17

Changed

  • Optimized cmake
  • Secondary alignments are filtered now

Added

  • Output UMIs with only exonic or only intronic reads

[0.6.8] - 2017-09-22

Added

  • Filtration of reads by barcode quality ("TagsSearch/Processing/min_barcode_quality" and "Estimation/Other/min_barcode_quality" fields in the config)
  • dropEst is now able to parse read type (e.g. exonic/intronic) from .bam file (see config_desc.xml)

[0.6.7] - 2017-09-13

Changed

  • Fixed bug, which led to erroneous parsing of incorrect read (e.g. reads without spacer for Indrop V1)

Added

  • Parallelized dropTag ("-p" option)

[0.6.5] - 2017-09-07

Changed

  • Optimized memory usage and performance of dropEst
  • Sorting for cells selection (by number of genes) is stable now
  • Fixed bug with merge_targets in low-quality cells estimation
  • Fixed bug with N's in UMIs after the merge

[0.6.1] - 2017-09-05

Added

  • Support for pseudoaligners .bam format (usage of chromosome name as a source of gene name)
  • Changelog

Changed

  • Check R libraries immediately after dropEst start

[0.6.0] - 2017-09-04

Added

  • Versioning