Input data for Coalispr
Creators
Description
Datasets to illustrate the use of Coalispr, a Python tool to clean up (small) RNA sequencing results. Coalispr can visualize over 100 bedgraphs in one panel and helps to retrieve read counts from associated alignment files without reliance on reference features like GTF annotations. The archives contain bedgraphs (also in processed form), reference data, bam-alignment files for counting, and descriptions for experiments, ncRNAs and genes.
Abstract
Datasets of STAR-mapped RNA-seq reads for analysis with Coalispr as described in the essay "Bio informatics: Integrate negative controls to get the good data." Preparation and analysis are detailed in the tutorials "Cryptococcus siRNAs", and "Mouse miRNAs".
Unprocessed fungal datasets were retrieved from GEO GSE128009 and GSE43363 and have been published by Dumesic et al. 2013 (DOI 10.1016/j.cell.2013.01.046) and Burke et al. 2019 (DOI 10.1534/g3.119.400330). Additional resources were gene-annotations from Wallace et.al 2020 (DOI 10.1093/nar/gkaa060) and data at GEO GSE133125.
Mouse data have been described in Sarshad et al. 2018 (DOI 10.1016/j.molcel.2018.07.020) and raw miRNA sequencing reads were kindly provided by the corresponding author, Markus Hafner.
Files
Files
(7.0 GB)
| Name | Size | Download all |
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md5:2bfd3a21b476dc6814c7c2bcf23dabfb
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5.4 GB | Download |
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md5:a27b7d279eea6a2faec14ac88f3827e2
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1.6 GB | Download |
Additional details
Software
- Repository URL
- https://codeberg.org/coalispr
- Programming language
- Python, Shell, Markdown, reStructuredText
- Development Status
- Active