What styles are available for the data tracks in views like Region in Detail?
To view data along a genomic region, you can choose from different styles using the 'Configure this page' menu in the Region in detail view. You can also hover over the track names and then the tool icon to view the style options for data which is already displayed.
Some tracks will only give you the option to turn them on or off (such as %GC, Contigs, and Structural variants). However, other data types give you more options. Below is a list of the track types available for different data types. Try them out to see if they suit your needs.
- No exon structure without labels - All transcripts are merged into a solid block with no differentiation between exons and introns
- No exon structure with labels - Same as above, with the gene name written under the block.
- Expanded without labels - Individual transcripts are shown aligned to the genome, with exons and introns clearly marked, with no names below the transcript (click on a transcript for more information).
- Expanded with labels - The standard, default expanded view. As above, with the transcript name written below.
- Collapsed without labels - One representative 'gene' is shown as one diagram with all possible exons represented, rather than individual transcripts.
- Collapsed with labels - As above, with the gene name written underneath the structure.
- Coding transcripts only - No non-coding transcripts are shown in the track.
ESTs, protein alignments, oligo probes and RNA-Seq intron spanning reads
- Variable height (intron-spanning reads only) - The density of reads is shown as a histogram. Non-canonical reads are shown in red.
- Normal - The standard, expanded format, showing a maximum of 7 features aligned against the genome with no names or IDs (click on the image to see the name or ID).
- Labels - As 'Normal', with labels added underneath each feature alignment.
- Half height - A maximum of 20 features are drawn, showing each alignment with a thinner bar than 'Normal'.
- Stacked - The features are shown very thin, and the differentiation between each one is lost.
- strong>Stacked unlimited - All features in the region are shown (rather than 7 or 20).
- Ungrouped - Feature ends will not be connected. Only the ends will be shown, aligned to the genome.
- No labels - Individual predictions are shown aligned to the genome, with exons and introns clearly marked, with no names shown (click for more information).
- With labels - As above, with labels below.
- Peaks - Points on the genome where the event (e.g. Histone modification, transcription factor binding) reaches a threshold, as measured by Chip-Seq.
- Signal - Histograms showing the frequency of the event (e.g. Histone modification, transcription factor binding) along the genome as measured by Chip-Seq.
- Both - Both of the above.
SNPs and indels variants
In all styles, variants are shown with consequences indicated by a colour code. Insertions are shown as a small arrow underneath.
- Normal (collapsed over a window if 200kb) - In a window greater than 200kb, variants are shown in the 'collapsed' style. In a window smaller than 200kb, variants are shown in the 'expanded without name' style.
- Collapsed - All variants are shown in a single line. Click on a variant to find out more.
- Expanded without name - Variants are spaced between multiple lines to show each one individually. Click on a variant to find out more.
- Expanded with name (hidden over a window of 10kb) - Variants are spaced between multiple lines to show each one individually. In a window less than 10kb, name labels are also shown.
- Compact - The presence of SVs is indicated in black bars in a single. Click on the bar to see how many SVs there are at the region.
- Expanded - Individual SVs are shown over multiple lines. Colour codes indicate the type of SV.
- Normal - BAM files from RNA-Seq experiments. A maximum of 50 reads are shown at each position. A histogram showing summarising the number of reads at each base position is shown above. If you zoom in, the sequence is shown on both the BAM reads and histogram, with mismatches between the read and the genomic sequences hightlighted in red.
- Unlimited - Similar to the 'Normal' view, but with a maximum of 500 reads.
- Coverage only - The histogram only is shown.
RNA-Seq gene models
- Expanded without labels - Individual predictions are shown aligned to the genome, with exons and introns clearly marked, with no names shown (click for more information).
- Expanded with labels - As above, with names and biotype predictions shown below.
BLAST and translated BLAT alignments
- Compact - Alignments are shown on a single line with no links between them.
- Normal - Alignments are spread between multiple strands and alignment structures are shown, with empty boxes indicating gaps in the alignment and gaps indicating gaps in the assembly.
- No labels - The position of the feature without labels.
- Normal - This is the default setting which varies depending on the track.
- Labels - The position of the feature with labels underneath.