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07.17.2017

Documentation outlining our RNA-Seq schema.

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03.27.2017

PIVOT released (replacing IDV); an extensive R-based GUI for the visualization and analysis of RNASeq data.

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11.09.2016

PESS has been released and is available for download with source code.

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03.02.2016

VERSE RNASeq quantifier has been released and is available for download.

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VERSE

Maintained by Qin Zhu License (GNU)

A versatile and efficient RNA-Seq read counting tool

VERSE is designed for high-performance read summarization for next generation sequencing. VERSE is 50x faster than HTSeq when computing the same gene counts. It introduces a novel, hierarchical assignment scheme, which allows simultaneous quantification of multiple feature types or annotation levels without repeatedly assigning reads. There is also a set of parameters the user can use to fine-tune the assignment logic. VERSE can be readily incorporated into any existing RNA-Seq analysis pipelines.

VERSE is implemented in C. It is built on top of featureCounts. VERSE supports Mac OSX and linux systems.

Publication: Zhu, Q., Fisher, S.A., Shallcross, J., Kim, J. (Preprint). VERSE: a versatile and efficient RNA-Seq read counting tool. bioRxiv 053306.
doi: http://dx.doi.org/10.1101/053306

Feature Summary

  • VERSE supports the following modes of RNA-Seq quantification:
    • FeatureCounts (Default)
    • HTSeq Union (-z 1)
    • HTSeq Intersection-strict (-z 2)
    • HTSeq Intersection-nonempty (-z 3)
    • VERSE Union-strict (-z 4)
    • VERSE Cover-length (-z 5)
  • Supported Quantification Schemes:
    • Hierarchical Assign -- assign reads to feature types according to their priority.
    • Independent Assign -- assign reads to feature types independently in a single run.

Update Log

    • v1.0.5 - Bug Fixed: Corrected counting for Non-unique mapped reads. New Feature: --multithreadDecompress. (9/10/2015)
    • v1.0.4 - Bug Fixed: Fixed crash cases where there are no unprocessed reads but thread was initiated; fixed merging of WASH6P. New Feature: --nonemptyModified. (7/14/2015)
    • v1.0.3 - Bug Fixed: Only one read in a BGZF chunk situation. (6/30/2015)

Download


Installation:

    • cd to the src folder, use make to compile the code.

      For Linux OS, use command::

      make -f Makefile.Linux

      For Mac OS, use command:

      make -f Makefile.MacOS

Usage

    • Please run ./verse to see the details.

      A sample command:

      ./verse -a testdata/test.gtf -t 'exon' -g gene_id -z 3 -s 1 -o testdata/intersection_nonempty.stranded.paired testdata/PE.sam

      A sample hierarchical assign command:

      ./verse -a testdata/test.gtf -t 'exon;intron;xine' -g gene_id -z 3 -o  testdata/intersection_nonempty.unstranded.paired.hierarchical testdata/PE.sam
    • User Manual (html)

Screen shots

(Click on images for larger version)

A sample hierarchical assignment which assigns all reads to exon, antisense exon, intron, antisense intron and intergenic regions sequentiallly in a single run.