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| Status |
Public on Aug 04, 2021 |
| Title |
RiboDoc: a Docker-based package for ribosome profiling analysis |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Ribosome profiling (RiboSeq) has emerged as a powerful technique for studying the genome-wide regulation of translation in various cells. Several steps in the biological protocol have been improved, but the bioinformatics part of RiboSeq suffers from a lack of standardization, preventing the straightforward and complete reproduction of published results. Too many published studies provide insufficient detail about the bioinformatics pipeline used. The broad range of questions that can be asked with RiboSeq makes it difficult to use a single bioinformatics tool. Indeed, many scripts have been published for addressing diverse questions. Here, we propose a unique tool (for use with multiple operating systems, OS) to standardize the general steps that must be performed systematically in RiboSeq analysis, together with the statistical analysis and quality control of the sample. The data generated can then be exploited with more specific tools. We hope that this tool will help to standardize bioinformatics analyses pipelines in the field of translation.
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| Overall design |
comparison between a WT yeast strain and a strain in which the frameshiffted OAZ1 gene has been replaced by an in-frame version of OAZ1
|
| Web link |
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8141510/
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| |
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| Contributor(s) |
François P, Arbes H, Demais S, Baudin-Baillieu A, Namy O |
| Citation(s) |
34093996 |
| |
| Submission date |
May 04, 2021 |
| Last update date |
Aug 05, 2021 |
| Contact name |
Olivier Namy |
| E-mail(s) |
[email protected]
|
| Organization name |
CNRS, Université Paris-Sud
|
| Department |
I2BC
|
| Lab |
Genomic, structure and Translation
|
| Street address |
Rue Gregor Mendel, bat 400
|
| City |
Orsay |
| ZIP/Postal code |
91400 |
| Country |
France |
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| Platforms (1) |
| GPL13821 |
Illumina HiSeq 2000 (Saccharomyces cerevisiae) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA727314 |
| SRA |
SRP318454 |
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