Manual

Introduction

  1. Search for a valid GENCODE ID (ENSG* , ENST* ) or a gene symbol. 1.1. For transcripts (ENST*), you can choose if you want the complete genomic context of the transcript or a relative view. 1.2 In the transcript-relative view,
    • Introns will be removed and
    • reverse-stranded transcripts will be inverted to forward-stranded.

You can specify an artificial spacing for the exons in the transcript-relative view. The spacing is defined as the fraction of the whole length of the transcript (for example, spacing of 0.2 will introduce equally spaced introns with a length equivalent to 20% of the exonic region length).

  1. Select datasets. For subdivided datasets (with a suffix _by*), you can click on the name and select the subdatasets of interest.
  2. Outputs and adjusting figure aesthetics. ElementaLdb will produce the following files:
  3. Generated figure and redrawing panel.
  4. Interactive annotation table.
  5. Interactive IGV browser session.

  6. Downloadable files: generated figure, IGV XML session, annotation in BED and CSV formats, and intermediate annotation files.

  7. Refine output figure in a local setting. If you want to further customize your plot, the downloadable zip folder contains everything for running ezTracks (https://github.com/HugoGuillen/ezTracks) or pyGenomeTracks (https://github.com/deeptools/pyGenomeTracks) locally.

For citations on the available datasets please visit the cite page.

Using GENCODE version 37