| Title |
METHimpute: imputation-guided construction of complete methylomes from WGBS data
|
|---|---|
| Published in |
BMC Genomics, June 2018
|
| DOI | 10.1186/s12864-018-4641-x |
| Pubmed ID | |
| Authors |
Aaron Taudt, David Roquis, Amaryllis Vidalis, René Wardenaar, Frank Johannes, Maria Colomé-Tatché |
| Abstract |
Whole-genome bisulfite sequencing (WGBS) has become the standard method for interrogating plant methylomes at base resolution. However, deep WGBS measurements remain cost prohibitive for large, complex genomes and for population-level studies. As a result, most published plant methylomes are sequenced far below saturation, with a large proportion of cytosines having either missing data or insufficient coverage. Here we present METHimpute, a Hidden Markov Model (HMM) based imputation algorithm for the analysis of WGBS data. Unlike existing methods, METHimpute enables the construction of complete methylomes by inferring the methylation status and level of all cytosines in the genome regardless of coverage. Application of METHimpute to maize, rice and Arabidopsis shows that the algorithm infers cytosine-resolution methylomes with high accuracy from data as low as 6X, compared to data with 60X, thus making it a cost-effective solution for large-scale studies. METHimpute provides methylation status calls and levels for all cytosines in the genome regardless of coverage, thus yielding complete methylomes even with low-coverage WGBS datasets. The method has been extensively tested in plants, but should also be applicable to other species. An implementation is available on Bioconductor. |
X Demographics
The data shown below were collected from the profiles of 9 X users who shared this research output. Click here to find out more about how the information was compiled.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Germany | 5 | 56% |
| Netherlands | 1 | 11% |
| United States | 1 | 11% |
| Unknown | 2 | 22% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Members of the public | 8 | 89% |
| Scientists | 1 | 11% |
Mendeley readers
The data shown below were compiled from readership statistics for 51 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Unknown | 51 | 100% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Student > Ph. D. Student | 15 | 29% |
| Researcher | 10 | 20% |
| Student > Master | 7 | 14% |
| Student > Bachelor | 4 | 8% |
| Student > Postgraduate | 2 | 4% |
| Other | 5 | 10% |
| Unknown | 8 | 16% |
| Readers by discipline | Count | As % |
|---|---|---|
| Agricultural and Biological Sciences | 18 | 35% |
| Biochemistry, Genetics and Molecular Biology | 10 | 20% |
| Computer Science | 4 | 8% |
| Engineering | 2 | 4% |
| Unspecified | 2 | 4% |
| Other | 4 | 8% |
| Unknown | 11 | 22% |
Attention Score in Context
This research output has an Altmetric Attention Score of 4. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 10 July 2019.
All research outputs
#6,893,001
of 23,088,369 outputs
Outputs from BMC Genomics
#3,104
of 10,705 outputs
Outputs of similar age
#118,650
of 329,367 outputs
Outputs of similar age from BMC Genomics
#70
of 250 outputs
Altmetric has tracked 23,088,369 research outputs across all sources so far. This one has received more attention than most of these and is in the 69th percentile.
So far Altmetric has tracked 10,705 research outputs from this source. They receive a mean Attention Score of 4.7. This one has gotten more attention than average, scoring higher than 70% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 329,367 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 63% of its contemporaries.
We're also able to compare this research output to 250 others from the same source and published within six weeks on either side of this one. This one has gotten more attention than average, scoring higher than 70% of its contemporaries.