Table 2 Description of Tools within riboStreamR

Data Upload

The tool allows users to upload their RNA-seq, Ribo-seq, annotation, and fasta files. After data upload and pre-processing, it displays a table with the number of alignments within each of the uploaded BAM files.

Summary Table

The tool provides a table with summary statistics for each sample, including total number of alignments, percentage of uniquely mapped reads, feature percentages, complexity, duplication values, and periodicities.

Read Length

Computes read length distributions for any combination of input files or data subsets.

GC %

Computes GC percentage distributions for any combination of input files or data subsets.

Feature %

Generates bar charts of the relative numbers of alignments mapping to the different feature types or any other alignment attribute.

Single Gene

Visualizes the read densities within single genes. Genes are displayed in genomic coordinates with gray regions indicating exons. Density bars can be color coded to differentiate between data subsets.

Meta Periodicity

The tool generates a meta gene distribution around the TSS and TSC for a single sample, showing the read density at each nucleotide. This is useful for gauging the level of periodicity.

Sample Meta Distribution

Generates line graphs of the distribution of reads around the TSS and stop codon. The tool allows users to compare multiple samples or other read subsets.

Length Periodicity

Computes a bar graph that shows the relative number of alignments within each frame.

Differential Analysis

The tool computes a table which contains RPKM values for each gene, as well as the results of a differential analysis using edgeR, including the logFC, P-value, and FDR. Can perform differential expression or translation analyses.

Report Generator

The tool generates a report containing the outputs of the user selected tools, as well as the parameters used to produce the output, a description of the processing methods, and any user-provided notes.