التفاصيل البيبلوغرافية
| العنوان: |
Unique kmer counts (y-axis) of specified length (x-axis) extracted from simulated reads. |
| المؤلفون: |
Raquel Linheiro (11747717), John Archer (235004) |
| سنة النشر: |
2021 |
| المجموعة: |
Smithsonian Institution: Digital Repository |
| مصطلحات موضوعية: |
Genetics, Molecular Biology, Ecology, Inorganic Chemistry, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, related side study, div >< p, differentially expression genes, de bruijn based, cdna transcripts represented, ambiguous paths exist, mapped read counts, serinus canaria <, rattus norvegicus <, panthera pardus <, de novo <, underlying graph structure, similar classification systems, representing two adult, drosophila melanogaster <, within reference sets, assembling read data, sequence information stored, chimeric contigs based, assembled using cstone, melanogaster <, read data, underlying graphs, sequence identity |
| الوصف: |
Reads were simulated from the four species (indicated on right) as described under the “Demonstration” heading of the Design and Implementation section of the manuscript. Above kmer size of 18 little difference is observed in the number of unique kmers extracted. Kmer sizes from 1 to 18 show a marked increase as kmer frequency as size is incremented in steps of 1. This indicates that for these small kmers, shared kmers by chance (or kmer collisions) between different gene families and gene regions are more likely. For example, for kmer sizes of 4 there are only 256 unique permutations to describe the entire read dataset. Assemblies using kmers of this size would produce spurious sets of contigs that are highly chimeric. The three assemblers used in this study were Trinity, CStone and rnaSPAdes and have default kmer sizes of 25, 40 and 55 respectively, as indicated with the dashed vertical lines. (TIF) |
| نوع الوثيقة: |
still image |
| اللغة: |
unknown |
| Relation: |
https://figshare.com/articles/figure/Unique_kmer_counts_y-axis_of_specified_length_x-axis_extracted_from_simulated_reads_/17071703 |
| DOI: |
10.1371/journal.pcbi.1009631.s001 |
| الاتاحة: |
https://doi.org/10.1371/journal.pcbi.1009631.s001 |
| Rights: |
CC BY 4.0 |
| رقم الانضمام: |
edsbas.FF6D4082 |
| قاعدة البيانات: |
BASE |