GNomEx

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GNomEx is a web tool for organizing, annotating, tracking, and distributing raw genomic data and associated downstream analysis. It contains a genomic LIMS, an Analysis Project Center, and Programmatic Data Distribution Server. See Nix et. al.'s paper for details.


Use GNomEx to store your raw experimental data and any associated analysis for manual and programmatic data access by the B2B community.


Click here to launch the B2B GNomEx instance B2B GNomEx instance.

Bugs? Feature Requests? If you don't have an account on our issue tracking (JIRA) system, email gnomex.support@hci.utah.edu to request an account.

Old site for: Bugs? Feature Requests?

Help! Forum

Contents

GNomEx Help

Application Quick Start Guides

Supported GNomEx Data Track File Formats

Alignments: BAM

  • Use the Picard SortSam.jar application to sort by coordinate and index your alignment file. SAMTools does not work. Both the sorted xxx.bam and associated xxx.bai index file are required.
  • Example: java -jar -Xmx10G ~/Software/picard-tools-1.56/SortSam.jar SO=coordinate CREATE_INDEX=true TMP_DIR=. I=7940X13_81BNAABXX_8.sam O=7940X13_81BNAABXX_8.bam
  • Common mistake: listing chromosomes as 1,2,3,4...; these need to be chr1, chr2, chr3...; referencing the mitochondria chromosome as anything other than chrM; check the sam header


Region data: (e.g. chr start stop ... including bed12): xxx.useq and UCSC's bigbed xxx.bb format

  • Data is best uploaded using the xxx.useq format. This is a compressed, indexed binary format, with no floating point restriction, typically 25-50% the size of bb. It is compatible with both DAS/2 (IGB browser) and, through auto conversion, to bb in GNomEx with the UCSC and IGV genome browsers. Use the Text2USeq, Wig2USeq, and UCSCBig2USeq apps to convert. Alternatively, UCSC's bigBed bb formatted files may be uploaded, although these are not DAS/2 compatible. A bb to useq auto converter is in the works but currently not implemented....


Graph data: xxx.useq and xxx.bw (e.g. chr position ....) data

  • Data is best uploaded using the useq format, see above. Alternatively, UCSC's big wig formatted files may be uploaded, although these are not DAS/2 compatible and 1.5-2x bigger than useq.


Large genome sequence data: bnib

  • Follow this FAQ to convert fasta data to bnib


Gene annotations: brs

  • Follow this FAQ to convert refflat or refseq gene tables to binary refflat.


Other binary indexed file formats can be requested.


GNomEx Release Notes

All GNomEx Release notes can be found here

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