bioinfo_report_Riboseq.knit

Bioinformatics Service Report

IMMAGINA Biotechnology S.r.l.

Sales Order No.: SOXXXXXXX

Order No.: POXXXXXXX

07/04/2025

Thank you for choosing IMMAGINA Biotechnology for your analysis needs! This interactive report provides a comprehensive overview of your results, with easy-to-read graphs and charts that bring your data to life.

If you have any questions about the analyses, please don’t hesitate to contact us at bioinformatics@immaginabiotech.com

Workflow

Reference genome version: https://www.gencodegenes.org/human/release_42.html (Comprehensive gene annotation))

For more details on the output plots, refer to https://github.com/ImmaginaBiotechnology/Documents/blob/main/Martian.md

1. Removal of rRNA, tRNA and snRNA reads

Table 1:

Number and Percentage of reads aligned on rRNA, tRNA and snRNA databases respect to the total number of trimmed reads.

2. Alignment Statistics

Table 2:

Percentage of reads uniquely and multi aligned to the transcriptome after rRNA, tRNA, snRNA and PCR duplicates removal.

3. Riboseq QC

‘Read Length Distibution’ plot shows the read length distribution respect to total reads. RPFs are generally between 30nt and 40nt length (depends on conformation) and disomes are generally between 70 nt and 90 nt.

‘Read Region & Frame’ plot shows the percentage of P-sites mapping to the 5′ UTR, coding sequence (CDS), and 3′ UTR corresponding to the three possible reading frames.

‘Heatmap (Normalized on Total Reads)’ plot shows the percentage of P-sites corresponding to the three possible reading frames along the 5′ UTR, CDS, and 3′ UTR, stratified for read length. The percentage is normalized on the total number of reads.

‘Heatmap (Normalized inside each Read Length)’ plot shows the percentage of P-sites corresponding to the three possible reading frames along the 5′ UTR, CDS, and 3′ UTR, stratified for read length. For each length and each region, the sum of the signal is normalized to 100%.

Martian QC Report

4. Riboseq Global

‘Metaprofile’ plot shows P Site positions for all transcripts around translation initiation sites (TISs, from 0 to 100 nt) and translation termination sites (TTSs, from 0 to -100 nt) highlighted with a red line.

‘Covered Area’ plot shows for every transcript (each column) the percentage of the total length covered at least 1 read.

‘Codon Usage’ plot show the frequency of in-frame P-sites along the coding sequence associated to each codon, normalized for codon frequency in sequences.

Martian Global Report

5. Outputs

* Raw Data

* MultiQC html report

* BAM files

* Table with n° of reads for each transcript

* Table with n° of in-frame reads for each transcript

* Table with psite information for each read

* Plots

6. Download results

30 days after the data delivery, we will delete outdated data. So please keep your data properly. If you have any questions or concerns, please contact us as soon as possible.