The ppRNome Genome Browser displays experimental data introduced in the paper :
Whole-genome mapping of 5' ends in bacteria by tagged sequencing: A comprehensive view in Enterococcus faecalis N. Innocenti, M. Golumbeanu, A. Fouquier d'Hérouël, C. Lacoux, R. A. Bonnin, S. P. Kennedy, F. Wessner, P. Serror, P. Bouloc, F. Repoila and E. Aurell [RNA, 2015] Bioproject PRJNA272574
Navigation: Select the region you want to see on the 'Overview' track. Drag the window on the 'Region' track to pan the view. The ruler on the 'Details' track can be clicked on and is useful to compare data on many tracks. Clicking on 'Genes' or 'CDS' opens a new window/tab with annotated function and sequence.
Display: Choose the data you want to visualize in the 'Select Tracks' menu above, where brief track descriptions are available. You can also upload your own annotations in the 'Custom Tracks' menu. Adapt the display to your screen in the 'Preferences'. To customize a specific track, click on the tool button . Tracks can be dragged up and down.
Any combination of datatracks can be selected. However, activating a large number of tracks may slow down the interactive navigation or put the server on high load, typically causing some of tracks to be replaced by a pink ribbon containing an error message. In such cases, simply wait a few seconds and use the refresh button of your web browser to reload the page.
All tracks associated with a given transcriptome are presented in a similar color (green for KTH, orange for KTHr, red for St and blue for Rt). In each case, a darker version of the color is used to represent the reverse strand.
Most of the available quantitive track use a scale automatically adjusted to the region displayed in the browser, independently for each track. The scale can be viewed by moving the slider in the "Region" navigation bar to its right-most position. While this is most convenient for usual browsing, the automatic scaling is not suitable for quantitive comparison between tracks or regions. When doing so, please consider setting the scale manually by clicking on the 'wrench' icon.
Please note that when viewing large region of the genome (large meaning more nucleotides than pixels in the width of the plot), GBrowse performs some sort of averaging of data over small windows in order to downscale the data to a suitable resolution for display, which may affect the numerical values displayed. Consequently, users interested in accurate quantitative data are highly advised to consider using small regions (on the order of 1 kbp).
Raw data available displayed in the browser can be downloaded here for offline use.
1. Annotation
Genomic annotation and other information available from E. faecalis V583 complete genome sequence at NCBI Genbank, reference AE016830, AE016831 and AE016833
2. Transcriptional Profiles (TP)
Strand specific transcriptional profiles (TP) for the four transcriptomes. The presence of the black bar underneath the graph emphasizes that no signal was detected at the location, helping to distinguish regions with low but non-zero coverage. The signals displayed represent max(log10(x),-1) , where x is the raw coverage signal obtained as described in the main paper. No normalization is applied.
3. TSS and PSS tags signals
The TSS and PSS tracks show the count of corresponding tags found in St and Rt, with a cutoff at 255 (in order to overcome issues with large dynamic ranges in GBrowse). Values above 5 in St and 7 in Rt are emphasized in green, more or less reproducing the significance threshold used in the paper.
The Alt. TSS/PSS tracks provide an alternative an somewhat more intuitive way of visualizing tag signals. The intensity of the color on the track represents y = 100 * x^2 / ( x^2 + 5^2 ) where x is the normalized tag signal, i.e. expressed in number of tags per million tagged reads mapped.
4. Helper tracks
Tracks presenting processed Raw data, useful for interpretation of the data :
Angle : the track presents the value of atan(PSS/TSS) in degrees, i.e. the angle at which the point is located in figure 2 in the paper, if the tag signal at the corresponding position is greater than 3.2 per million tagged reads aligned (see paper), and -1 otherwise. Values above 45° are emphasized in green.
Multimap : the color intensity of the track shows the fraction (in %) of multiply mapped reads at the corresponding position. The value for the RtSt tracks are the maximum of the values of St and Rt, and the one for KTH track is the maximum of KTH and KTHr. A large fraction of multiply mapped reads means that the signals at the corresponding locus cannot be interpreted without additional information from other experiments.
5. Transcription Profile Comparison
A series of plots aiming at comparing transcription profiles across transcriptomes. The plots show max(log10(y),-1) where y is the normalized coveraged expressed in reads per 100 million of reads mapped.
. Tracks can be dragged up and down.
