| Autor: |
Sihan Zhen, Hongwei Zhang, Yuxin Xie, Song Zhang, Yan Chen, Riliang Gu, Sanzhen Liu, Xuemei Du, Junjie Fu |
| Jazyk: |
angličtina |
| Rok vydání: |
2022 |
| Předmět: |
|
| Zdroj: |
Plants, Vol 11, Iss 14, p 1821 (2022) |
| Druh dokumentu: |
article |
| ISSN: |
2223-7747 |
| DOI: |
10.3390/plants11141821 |
| Popis: |
Although bulked segregant analysis (BSA) has been used extensively in genetic mapping, user-friendly tools which can integrate current algorithms for researchers with no background in bioinformatics are scarce. To address this issue, we developed an R package, PNGSeqR, which takes single-nucleotide polymorphism (SNP) markers from next-generation sequencing (NGS) data in variant call format (VCF) as the input file, provides four BSA algorithms to indicate the magnitude of genome-wide signals, and rapidly defines the candidate region through the permutation test and fractile quantile. Users can choose the analysis methods according to their data and experimental design. In addition, it also supports differential expression gene analysis (DEG) and gene ontology analysis (GO) to prioritize the target gene. Once the analysis is completed, the plots can conveniently be exported. |
| Databáze: |
Directory of Open Access Journals |
| Externí odkaz: |
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