smalldisco, a pipeline for siRNA discovery and 3' tail identification.
| Autor: | Caldas IV; Department of Molecular Biology and Genetics, Cornell University, 526 Campus Rd, Ithaca, NY 14850, USA.; Department of Biology, Syracuse University, 107 College Place, Syracuse, NY 13210, USA., Kelley LH; Department of Biology, Syracuse University, 107 College Place, Syracuse, NY 13210, USA., Ahmed-Braimah YH; Department of Biology, Syracuse University, 107 College Place, Syracuse, NY 13210, USA., Maine EM; Department of Biology, Syracuse University, 107 College Place, Syracuse, NY 13210, USA. |
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| Jazyk: | angličtina |
| Zdroj: | G3 (Bethesda, Md.) [G3 (Bethesda)] 2023 Jun 01; Vol. 13 (6). |
| DOI: | 10.1093/g3journal/jkad092 |
| Abstrakt: | Capturing and sequencing small RNAs is standard practice; however, identification of a group of these small RNAs-small interfering RNAs (siRNAs)-has been more difficult. We present smalldisco, a command-line tool for small interfering RNA discovery and annotation from small RNA-seq datasets. smalldisco can distinguish short reads that map antisense to an annotated genomic feature (e.g. exons or mRNAs), annotate these siRNAs, and quantify their abundance. smalldisco also uses the program Tailor to quantify 3' nontemplated nucleotides of siRNAs or any small RNA species. smalldisco and supporting documentation are available for download from GitHub (https://github.com/ianvcaldas/smalldisco) and archived in Zenodo (https://doi.org/10.5281/zenodo.7799621). Competing Interests: Conflicts of interest statement The author(s) declare no conflict of interest. (© The Author(s) 2023. Published by Oxford University Press on behalf of The Genetics Society of America.) |
| Databáze: | MEDLINE |
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