Shoelaces: an interactive tool for ribosome profiling processing and visualization
Abstract Background The emergence of ribosome profiling to map actively translating ribosomes has laid the foundation for a diverse range of studies on translational regulation. The data obtained with different variations of this assay is typically manually processed, which has created a need for to...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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BMC
2018-07-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12864-018-4912-6 |
| _version_ | 1818333685267562496 |
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| author | Åsmund Birkeland Katarzyna ChyŻyńska Eivind Valen |
| author_facet | Åsmund Birkeland Katarzyna ChyŻyńska Eivind Valen |
| author_sort | Åsmund Birkeland |
| collection | DOAJ |
| description | Abstract Background The emergence of ribosome profiling to map actively translating ribosomes has laid the foundation for a diverse range of studies on translational regulation. The data obtained with different variations of this assay is typically manually processed, which has created a need for tools that would streamline and standardize processing steps. Results We present Shoelaces, a toolkit for ribosome profiling experiments automating read selection and filtering to obtain genuine translating footprints. Based on periodicity, favoring enrichment over the coding regions, it determines the read lengths corresponding to bona fide ribosome protected fragments. The specific codon under translation (P-site) is determined by automatic offset calculations resulting in sub-codon resolution. Shoelaces provides both a user-friendly graphical interface for interactive visualisation in a genome browser-like fashion and a command line interface for integration into automated pipelines. We process 79 libraries and show that studies typically discard excessive amounts of quality data in their manual analysis pipelines. Conclusions Shoelaces streamlines ribosome profiling analysis offering automation of the processing, a range of interactive visualization features and export of the data into standard formats. Shoelaces stores all processing steps performed in an XML file that can be used by other groups to exactly reproduce the processing of a given study. We therefore anticipate that Shoelaces can aid researchers by automating what is typically performed manually and contribute to the overall reproducibility of studies. The tool is freely distributed as a Python package, with additional instructions, tutorial and demo datasets available at https://bitbucket.org/valenlab/shoelaces. |
| first_indexed | 2024-12-13T13:55:34Z |
| format | Article |
| id | doaj.art-1b238bdf250e40cf9b36d39d4df2e76e |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-13T13:55:34Z |
| publishDate | 2018-07-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-1b238bdf250e40cf9b36d39d4df2e76e2022-12-21T23:42:54ZengBMCBMC Genomics1471-21642018-07-011911610.1186/s12864-018-4912-6Shoelaces: an interactive tool for ribosome profiling processing and visualizationÅsmund Birkeland0Katarzyna ChyŻyńska1Eivind Valen2Department of Informatics, University of BergenComputational Biology Unit, Department of Informatics, University of BergenComputational Biology Unit, Department of Informatics, University of BergenAbstract Background The emergence of ribosome profiling to map actively translating ribosomes has laid the foundation for a diverse range of studies on translational regulation. The data obtained with different variations of this assay is typically manually processed, which has created a need for tools that would streamline and standardize processing steps. Results We present Shoelaces, a toolkit for ribosome profiling experiments automating read selection and filtering to obtain genuine translating footprints. Based on periodicity, favoring enrichment over the coding regions, it determines the read lengths corresponding to bona fide ribosome protected fragments. The specific codon under translation (P-site) is determined by automatic offset calculations resulting in sub-codon resolution. Shoelaces provides both a user-friendly graphical interface for interactive visualisation in a genome browser-like fashion and a command line interface for integration into automated pipelines. We process 79 libraries and show that studies typically discard excessive amounts of quality data in their manual analysis pipelines. Conclusions Shoelaces streamlines ribosome profiling analysis offering automation of the processing, a range of interactive visualization features and export of the data into standard formats. Shoelaces stores all processing steps performed in an XML file that can be used by other groups to exactly reproduce the processing of a given study. We therefore anticipate that Shoelaces can aid researchers by automating what is typically performed manually and contribute to the overall reproducibility of studies. The tool is freely distributed as a Python package, with additional instructions, tutorial and demo datasets available at https://bitbucket.org/valenlab/shoelaces.http://link.springer.com/article/10.1186/s12864-018-4912-6Ribosome profilingBioinformaticsGenomicsPythonTool |
| spellingShingle | Åsmund Birkeland Katarzyna ChyŻyńska Eivind Valen Shoelaces: an interactive tool for ribosome profiling processing and visualization BMC Genomics Ribosome profiling Bioinformatics Genomics Python Tool |
| title | Shoelaces: an interactive tool for ribosome profiling processing and visualization |
| title_full | Shoelaces: an interactive tool for ribosome profiling processing and visualization |
| title_fullStr | Shoelaces: an interactive tool for ribosome profiling processing and visualization |
| title_full_unstemmed | Shoelaces: an interactive tool for ribosome profiling processing and visualization |
| title_short | Shoelaces: an interactive tool for ribosome profiling processing and visualization |
| title_sort | shoelaces an interactive tool for ribosome profiling processing and visualization |
| topic | Ribosome profiling Bioinformatics Genomics Python Tool |
| url | http://link.springer.com/article/10.1186/s12864-018-4912-6 |
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