Výsledky vyhledávání

0539495 - ÚBO DATA Vědecká data      2021
Bryja, Josef

Genomic ddRAD datasets of Ethiopian Lophuromys - raw data.

Popis: The files contain pair-end reads that were submitted to ipyrad (Eaton & Overcast, 2020) for denovo assembly of ddRAD loci. The reads were demultiplexed and barcodes removed in Skewer (Jiang, Lei, Ding & Zhu, 2014) and pre-processing of read ends in PEAR (Zhang, Kobert, Flouri & Stamatakis, 2014). Every pair of reads was merged (with minimum required overlap of 10 nucleotides) and cut in two halves. If they were not successfully merged, we trimmed off the last 10 nucleotides from the reverse read. The PEAR-treatment was necessary to avoid poor quality mergers in a substantial proportion of loci. The data are used and analysed in Komarova et al., submitted to Molecular Ecology.
Klíčová slova: ddRAD * Lophuromys * Ethiopia
Obor OECD: Zoology
DOI: https://doi.org/10.57680/asep.0539495
Handle: http://hdl.handle.net/11104/0317292
Vkladatel: Bryja, Josef
Datum publikování: 15.2.2021
 

0533584 - ÚBO DATA Vědecká data      2020
Bryja, Josef

Genomické ddRAD datasety etiopských Lophuromys.
[Genomic ddRAD datasets of Ethiopian Lophuromys.]

Popis: (1) Three alternative ddRAD datasets of concatenated SNPs used in ML phylogenetic analyses: (i) Complete data of 71341 SNPs/loci. (ii) Reduced data of 13 184 SNPs/loci present at least in 30% of individuals. (iii) Reduced data of 699 SNPs/loci present at least in 90% of individuals.
(2) Alternative ddRAD datasets used for sNMF analysis (in two formats - geno and nexus): (i) 13 586 loci present in 30% of genotyped ingroup individuals. (ii) 787 loci present in 90% of genotyped ingroup individuals.
The data are used and analysed in Komarova et al., submitted to Molecular Ecology.
[(1) Three alternative ddRAD datasets of concatenated SNPs used in ML phylogenetic analyses: (i) Complete data of 71341 SNPs/loci. (ii) Reduced data of 13 184 SNPs/loci present at least in 30% of individuals. (iii) Reduced data of 699 SNPs/loci present at least in 90% of individuals.
(2) Alternative ddRAD datasets used for sNMF analysis (in two formats - geno and nexus): (i) 13 586 loci present in 30% of genotyped ingroup individuals. (ii) 787 loci present in 90% of genotyped ingroup individuals.
The data are used and analysed in Komarova et al., submitted to Molecular Ecology.]
Klíčová slova: ddRAD * Lophuromys * Ethiopia
Obor OECD: Zoology
DOI: https://doi.org/10.57680/asep.0533584
Handle: http://hdl.handle.net/11104/0311955
Vkladatel: Bryja, Josef
Datum publikování: 28.10.2020