Additional options for a transcript ID

1. You can choose either the complete genomic context of the transcript or a relative view.

2. In the transcript-relative view:

   • introns are removed.

   • coordinates are transformed relative to the mature lncRNA.

   • reverse-stranded transcripts are inverted to forward-stranded.

3. Additionally, intron spacing can be specified for a better visualisation of exonic regions.

   • 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.

Outputs

1. The output figure is on the left side of the page and an interactive annotation table is displayed on the right side.

2. The transcripts and the overlapping elements are shown along with the parameters to customize and Redraw the figure.

3. Several additional options to browse the results are available below the table on the right side.

4. Interactive IGV session can be launched in the browser by clicking on IGV Browser.

5. File can be downloaded using the Download IGV session link, which can be used to run the IGV session on the local device.

6. The figure can be downloaded using the Download PDF link.

7. All the files, including the generated figure, IGV XML session, annotation in BED and CSV formats and intermediate annotation files, can be downloaded using the Download all files (ZIP) link.

8. To further customize the plot, run ezTracks or pyGenomeTracks locally using the files in the downloaded zip folder.