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Tutorial

Setup

image depicting login status/link and track configuration link
1) Data tracks are available based on user identity. Currently, "guest" (non-authenticated user) has no available data tracks. User id for active session is shown in upper right of screen. If user is not logged in, a login link appears in this area.
2) "Track Configuration" - this is an active link that will bring user to a page showing available projects and associated tracks that they can choose to view.

Track Configuration

Image shows the track configuration screen and controls
The track configuration page allows the user to specify which libraries' data will be analyzed and to control how it is displayed.
1) "Collapse Annotation" - if this box is checked, all isoforms for a given gene will be merged to create a single view of the gene. An example of collapsed versus expanded annotation is shown in the next image
2) These check boxes determine what library types will be included when rendering the D-plots
3) Library selection - each sequencing library is grouped with similar replicates under the parent project. The checkbox next to the library name determines ifs data will be shown. The "Color:" text box allows entry of a hexadecimal RGB value to designate what color to use for the library when drawing the D-plot. Clicking on the box will also bring up a graphic based color selector for ease of use. The "Opacity:" text box allows user to specify a value between 0 and 1 to determine how opaque the datapoints for the library will be painted on the D-plot. The default is .75 which allows clear visibility of each point without obscuring underlying points. The "tpXm:" box allows user to specify a scale for the data library where the value corresponds to the "X" in tpXm. Any "submit" button may be used to register changes. They all function identically and are repeated simply for convenience.

image depicting difference between collapsed and expanded annotation

Browsing

Browser image

The genome "Browser" tab shows a track per library view in a manner similar to other genome browsers (e.g., UCSC, ENSEMBL)
1) The "genome range" bow shows locii coordinates currently in view and allows user to specify a new position. "gene" box and "search" button allows user to search for a specific gene or isoform. The shift view controls allow user to shift up or downstream of current view by small and large size increments, as well as zoom in and out (*NOTE - high granularity zoom [to within only dozens of nucleotides] has known bugs and requires additional development).
2) The +strand area shows annotation (if exists) for the positive strand in the genome region displayed
3) Track data area shows a fixed height graph with an automatically adjusted scale (based on signal amplitudes in viewed region) for each track. All tracks are adjusted to same scale (min/max magnitudes labelled only for first track). Positive strand signal is depicted in red and drawn up from midline, negative strand signal depicted in green and drawn down from baseline. Signal whose value exceeds the track magnitude is terminated in a purple point (shown in expanded view within image). Each track's corresponding library name is shown as a label to the left of the data.
4) The -strand area shows annotation (if exists) for the negative strand in the genome region displayed

D-Plots

image depicting D-plot screens
The D-plot tab shows the region in view depicted as a D-plot style graph. A separate plot is rendered for each genome strand.
1) The color key for libraries as chosen in the Track Configuration screen

Searching

Search box
The gene box can be used to search by gene name(symbol) as shown here. Alternatively, user may enter a specific transcript name (e.g., "GAPDH-011") or transcript id (e.g., "ENST00000492719.1") or a portion thereof. Results page is shown in next image:
search results image
The search results list any annotation entries matching the search term entered in the "gene" box.
1) The magnifying glass figure and chart figure are active links and will take you to the genome browser or d-plot page for the associated transcript, respectively.

Mapping Report

Mapping report example

The mapping report shows all sequences represented by NGS reads in selected libraries within the region in view. The default presentation is sorted by library type (cap or monoP) and then by genomic position (*Please note, while it is theoretically possible that the same nucleotide sequence could appear in as part of both monoP and cap libraries, the data is not currently organized in such a manner as to combine these, so signal values under cap libraries for a monoP type sequence should always show as "0.0" and vice versa. In the case where the same nucleotide sequence occurs in both library types, a separate line will be shown for each type). The data in the report is generally self explanatory. Mismatch details are as reported by the Bowtie program. Transcripts must span the region of the mapping to be associated (on the same strand). Values in the library name headed columns are the tp1m signal attributed to the sequence for that library.
1) The chart figure is an active link that will allow user to downaload data shown on page to a Tab separated value text file that can be viewed in Excel. The download will also show a list of transcripts in the region at the top of the file.
2) The "Genome Hits" column contains active links that will display a page showing each locus the read could map to.
image shows report of additional genome mappings for sequence
This image shows page of genome hits for sequence that would appear if user clicked on "3" link in the previous image.