Caenorhabditis elegans trans-splicing

This repository contains the code used for generating the figures depicted in the following paper: Quantitative analysis of C. elegans transcripts by Nanopore direct cDNA sequencing reveals terminal hairpins in non trans- spliced mRNAs. Bernard, et al. 2022.

The manuscript is available on BioRxiv.

Authors

• Florian Bernard ¹𝄒²
• Delphine Dargere ¹
• Oded Rechavi ²
• Denis Dupuy ¹

¹ Université de Bordeaux, Inserm U1212, CNRS UMR5320 , Institut Européen de Chimie et Biologie (IECB), 2, rue Robert Escarpit, 33607 Pessac, France.

² Department of Neurobiology, Wise Faculty of Life Sciences & Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.

 

Data availability

The direct-cDNA datasets used in this study have been deposited in the Sequence Read Archive (SRA) under the following accession code: PRJNA822363.

The processed dataset, along with the necessary files for running the notebooks locally have been deposited on Figshare (DOI: 10.6084/m9.figshare.19131260).

 

Repository organization

A preprocessing notebook is available for generating the dataset table used in all downstream analysis from SAM/BAM alignments files (retrieved from our SRA archive or for analyzing your own alignment files).

A separate notebook was then generated for each of the figures shown in the paper as detailed above:

Notebook	Figure	Title
pre-processing	-	Pipeline for processing alignments and generating the dataset table
Fig1_notebook	Fig. 1b	Measure of base quality in 5' soft-clip region and alignment region
Fig2_notebook	Fig. 2b	Measure of total SL1 and SL2 variants detected in our reads
Fig3_notebook	Fig. 3a	Spliced leader usage
Fig3_notebook	Fig. 3b	SL2 gene specificity
Fig4_notebook	Fig. 4a	Gene expression and trans-splicing status
Fig4_notebook	Fig. 4b	Trans-splicing detection level
Fig4_notebook	Fig. 4c	Poorly trans spliced mRNA have a propensity to form a 5’ stem loop structure
Fig5_notebook	Fig. 5a	Measure of ratio SL/Hairpin
Fig5_notebook	Fig. 5b	Proportion of trans-spliced gene with various SL thresholds
Fig5_notebook	Fig. 5c	Read coverage for SL, Hairpin and Unidentified genes
Fig6_notebook	Fig. 6	Schematic representation of the trans-splicing information
SupFig1_notebook	Sup. Fig. 1	Measure of strand bias in direct-cDNA experiments
SupFig2_notebook	Sup. Fig. 2b	Measured length of 5’ and 3’ soft-clips
SupFig3_notebook	Sup. Fig. 3a	Quantification of sequencing adapters in soft-clips regions
SupFig3_notebook	Sup. Fig. 3b	Origin of supplementary alignments
SupFig3_notebook	Sup. Fig. 3c	Size distribution of supplementary alignments
SupFig4_notebook	Sup. Fig. 4	Measure of base quality across all sequencing experiments
SupFig5_notebook	Sup. Fig. 5a	Measure of read length and alignment length across experiments
SupFig5_notebook	Sup. Fig. 5b	Measure of read coverage
SupFig6_notebook	Sup. Fig. 6a	Strand orientation for unidentified reads
SupFig6_notebook	Sup. Fig. 6b	Length of 5’ soft-clips versus their alignment length
SupFig7_notebook	Sup. Fig. 7a	Single SL1 promotor - nlp-36 (B0464.3)
SupFig7_notebook	Sup. Fig. 7b	Multiple SL1 promotors - M60.4
SupFig7_notebook	Sup. Fig. 7c	Operon organization - rla-1 (Y37E3.8) & Y37E3.7
SupFig7_notebook	Sup. Fig. 7d	Differentially trans-spliced promoters - lev-11 (Y105E8B.1)
SupFig8_notebook	Sup. Fig. 8a	Measure of strand bias at each locus in SSP experiments
SupFig8_notebook	Sup. Fig. 8b	Unbiased locus presents a high concentration of SSP reads
SupFig8_notebook	Sup. Fig. 8c	Unbiased locus in SSP Exp. are found biased in SL1/NP Exp
SupFig9_notebook	Sup. Fig. 9	Method for evaluating base quality
SupFig10_notebook	Sup. Fig. 10	high confidence SL matchs are located near the alignment start

 

Generating your own plots

This web-app allows you to generate and save plots for your genes of interests without having to run the notebooks.
The app was made using the streamlit library (see streamlit_app.py) and is hosted via streamlit sharing.

 

License

The source code is licensed under the MIT License.