This document provides links to Supplemental Files and also a few guidelines to the proper manipulation of them.
This file is a Java application called Gaggle Genome Browser (GGB). You will need this application to open hbgb files (SuppFile 01 and SuppFile 02) and browse our data. Any Java distribution >= 6 should be enough to run the application. Here, I’m running the files using Ubuntu LTS 16.04 with OpenJDK 1.8.0_171 (Java version 8).
As any JAVA program, it works eqully fine in WINDOWS or MAC operation systems too, just click into it.
This hbgb file is essentially a SQLite database. The database is read by GGB to generate the genome visualization.
Every information required to open the genome browser is stored within this hbgb file, so you should download Supp File 00 and Supp File 01 to the same directory and run the following command line:
java -jar SuppFile_00_ggb_browser.jar -d SuppFile_01_intraRNAs.hbgbThis browser shows the distribution of relative numbers of aligned reads starting at a given genomic coordinate for TEX+ (blue) and TEX- (yellow) datasets (arbitrarily scaled log2 of normalized counts). Vertical bars that present blue and yellow are superimposed counts at the same position. Coding sequences in forward strand are depicted as yellow rectangles containing locus tag inside (5’→3’ direction is left to right). Coding sequences in reverse strand are depicted as orange rectangles (5’→3’ direction is right to left). PFAM domain annotation is represented by blue rectangles (ID inside). Identified iTSS are represented by green triangles, and transcription factor binding sites as red triangles. On the top and bottom, all possible archaeal start codons (green) and stop codon (red) are shown for forward and reverse strands, respectively.
Same type of file reported before for Supp File 01. The command line to open the browser should be:
java -jar SuppFile_00_ggb_browser.jar -d SuppFile_02_heatmaps.hbgbThis browser presents a heat map of tiling array expression profiles over the growth curve (time points are shown from top to bottom, Supplemental Figure 01). Coding sequences in forward strand are depicted as yellow rectangles containing locus tag inside (5’→3’ direction is left to right). Coding sequences in reverse strand are depicted as orange rectangles (5’→3’ direction is right to left). PFAM domain annotation is represented by blue rectangles (ID inside). Identified iTSS are represented by green triangles.
This BAM file contains all the aligments for TEX+ sequenced reads, i.e. every TEX+ sequencing library was aligned to the reference genome independently and merged using Samtools to generate this file. Note that this file has both single-end and paired-end alignments.
One may see the alignments by indexing it using Samtools and loading it in Integrative Genomics Viewer (IGV). Execute the following command line to index the file using Samtools:
samtools index -b SuppFile_03_texplus.bamAdditional files needed by IGV:
Reference Genome
Gene Annotation (not the same used in the paper)
This BAM file contains all the aligments for TEX- sequenced reads, i.e. every TEX- sequencing library was aligned to the reference genome independently and merged using Samtools to generate this file. Note that this file has both single-end and paired-end alignments.
This file should be loaded by the same way reported for Supp File 03.
This is a zip file containing several scripts used to obtain the results: