Commit 60f7965c authored by cziegenhain's avatar cziegenhain
Browse files

v2.9.7 update

parent c2be46d8

README.md

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@@ -31,6 +31,8 @@ We provide a script to convert zUMIs output into loom file automatically based o 
zUMIs will try to automatically do this, otherwise convert zUMIs output to loom by simply running `Rscript rds2loom.R myRun.yaml`.

zUMIs will try to automatically do this, otherwise convert zUMIs output to loom by simply running `Rscript rds2loom.R myRun.yaml`.





## Changelog

## Changelog

16 Jul 2021: zUMIs2.9.7: Change perl [shebang line](https://github.com/sdparekh/zUMIs/issues/261). Change featureCounts settings to assign reads to genes with the longest overlap in case of ambiguous/overlapping annotations. Allow to control the minimum required overlap of reads to genes with a setting `fraction_overlap:` in the counting section.



07 Apr 2021: zUMIs2.9.6: Fixed a potential crash when the input file to the barcode sharing feature does not contain an equal number of columns.

07 Apr 2021: zUMIs2.9.6: Fixed a potential crash when the input file to the barcode sharing feature does not contain an equal number of columns.





18 Feb 2021: zUMIs2.9.5: Mismatches for detecting Smart-seq3 UMI-read pattern are now user-settable in the YAML file as follows: `find_pattern: ATTGCGCAATG;2` would allow 2 mismatches. Usage as prior to this version (ie `find_pattern: ATTGCGCAATG`) will default to the previous value of 1 mismatch allowed.

18 Feb 2021: zUMIs2.9.5: Mismatches for detecting Smart-seq3 UMI-read pattern are now user-settable in the YAML file as follows: `find_pattern: ATTGCGCAATG;2` would allow 2 mismatches. Usage as prior to this version (ie `find_pattern: ATTGCGCAATG`) will default to the previous value of 1 mismatch allowed.

UMIstuffFUN.R

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@@ -584,6 +584,10 @@ fixMissingOptions <- function(config){ 
    config$counting_opts$multi_overlap <- FALSE

    config$counting_opts$multi_overlap <- FALSE

  }

  }





  if(is.null(config$counting_opts$fraction_overlap)){

    config$counting_opts$fraction_overlap <- 0

  }



  if(is.null(config$counting_opts$intronProb)){

  if(is.null(config$counting_opts$intronProb)){

    config$counting_opts$intronProb <- FALSE

    config$counting_opts$intronProb <- FALSE

  }

  }

correct_BCtag.pl

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#!/usr/bin/perl

#!/usr/bin/env perl

use warnings;

use warnings;





if(@ARGV != 4)

if(@ARGV != 4)

correct_UBtag.pl

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#!/usr/bin/perl

#!/usr/bin/env perl

use warnings;

use warnings;





if(@ARGV != 4)

if(@ARGV != 4)

fqfilter_v2.pl

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#!/usr/bin/perl

#!/usr/bin/env perl

# LMU Munich. AG Enard

# LMU Munich. AG Enard

# A script to filter reads based on Barcode base quality.

# A script to filter reads based on Barcode base quality.

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