Genome Annotations

Supported file format

RNAseqViewer can read annotations in two different formats: RefFlat and Gene Transfer Format (GTF).

RefFlat is used for example for RefSeq annotations provided by UCSC. The format consists in an eleven-column tab-delimited file, with one line per annotation (geneName, name, chrom, strand, txStart, txEnd, cdsStart, cdsEnd, exonCount, exonStarts, exonEnds).

GTF format is also supported. For faster loading in future sessions and faster gene search, RNAseqViewer will ask you the authorization to create an index file. The index file will be created in the same directory as the GTF file.

Alternatively, you can use the compressed GTF format. The original GTF file should be sorted, compressed with bgzip and indexed with Tabix, as in the following example:

(grep ^"#" in.gtf; grep -v ^"#" in.gtf | sort -k1,1 -k4,4n) | bgzip > sorted.gtf.gz;
tabix -p gff sorted.gtf.gz;

Compressed GTF files are faster for display operation, but are slower for searching a gene and for hiding intronic regions.

You can download human annotations on UCSC’s website in RefFlat format (hg18 and hg19). Ensembl’s website offers annotations for various species in GTF format (human genome and others). Human genome annotations can be downloaded from the Gencode Project website

Annotations can be displayed with two alternative types of view: Collapse View and Expanded View.

Collapse View

The Collapse View shows all the annotations on the same line. Thick lines represent exons and thin lines represent introns. The name of the gene is shown under the line and the other data are shown in a tool tip when hovering over the annotation or the name. Note that a version of the tool tip with links to reference websites can be activated (see Additional frames)

Expanded View

The Expanded View shows the annotations on several lines so as to avoid them to collapse.

../../_images/annotations.png

The annotations from the hg18 data set is displayed twice. The upper track shows the Collapse View and the lower track shows the Expanded View.

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Gencode 15 annotations. More information about the transcript under the mouse is displayed in the the side frame, with links to reference websites.