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Commits on Apr 24, 2017

• Merge pull request #8 from shenlab-sinai/develop_edd

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  eddielohyh

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Commits on Oct 6, 2015

• remove memory setting for samtools sort

  eddielohyh

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Commits on Aug 27, 2015

• modify README

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  221ec1d

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• modify README

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  abc0bb0

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• modify README

  eddielohyh

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  948d951

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• update flowchart

  eddielohyh

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• move makedir to a separate execution script so that errors from existing directories do not break the pipeline

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Commits on Aug 20, 2015

• remove unused files

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• revamp local processing script files to align with script-lsf files

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  07e0ddb

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• cleanup python.py file

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• add paired end alignment parsing, plus misc cleanup

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Commits on Jul 27, 2015

• add new config settings to determine uniqmapped, multimapped and unmapped reads.

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Commits on Jul 22, 2015

• add job completion comment to output to log file

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Commits on Jul 15, 2015

• amend result_parser.py regex for phantompeak.log to recognize negative values

  eddielohyh

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• add mapq and AS-XS cutoff option for splitting reads into unique and multi-mapped. amended results_parser.py to work after the changes

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Commits on Jul 10, 2015

• add setting for diffrepeat edit distance

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Commits on Jul 8, 2015

• modify fastqc to run from initial fastq files rather than bam files as bam files are now split among unmapped, uniquemapped and multimapped

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• Split alignments into uniquemapped, multimapped and unmapped bam files. Add diffRepeats analysis on unmapped and multimapped sequences. Reorganized the output directory structure and file locations

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Commits on Jul 7, 2015

• add diffRepeats analysis to pipeline

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• add repbase_db variable to config.yaml

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• correct error, we want to combine un and multimapped, NOT uniq and multimapped

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• merge uniq and multi-mapped bam files and generate fastq

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Commits on Jul 2, 2015

• add feature to split output alignment into unique-, multi-, and un-mapped bam files, first for bowtie2 single-end alignments

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Commits on Sep 9, 2014

• Merge pull request #7 from ny-shao/master

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• Update support for SGE, now the log file is normal.

  ny-shao

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Commits on Sep 5, 2014

• Merge pull request #6 from ny-shao/master

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• Update of README.

  ny-shao

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• SGE support is added.

  ny-shao

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• Merge pull request #5 from ny-shao/master

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• Fix a bug in pair end data.

  ny-shao

  committed
  cb50cee

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• Fix a bug in pair end data.

  ny-shao

  committed
  e23a608

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• Fix a bug in alignment of pair end data.

  ny-shao

  committed
  7509dea

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• Fix a bug in alignment of pair end data.

  ny-shao

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Commits on Aug 29, 2014

• Merge changes from https://github.com/shenlab-sinai/chip-seq_preprocess.

  

  Ningyi Shao

  committed
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Commits on Aug 16, 2014

• Remove unnecessary sorting in rmdup step (Fixes #3).

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