Commercial whole genome mapping systems, such as OpGen and BioNano, are playing an increasingly important role in a variety of genomic analyses, including de novo assembly, structural variant detection and assembly curation.
Comparison of a reference assembly to a collection of whole genome maps can help curators find potential regions of misassembly and identify genomic variations that are candidates for representation in alternate loci scaffolds. For example, optical maps played a key role in the GRC's resolution of the human 10q11.22 tiling path, as described in this prior GRC blog post.
To assist with curation efforts, the Wellcome Trust Sanger Institute, a GRC member, has integrated BioNano data sets for human, mouse and zebrafish assemblies into the gEVAL browser. They have also provided data from OpGen maps and optical maps from David Schwartz (PMID: 20534489). Common curation use cases for these browser data include:
Below is an example highlighting the potential usage.
The issue (HG-172) reports possible assembly error or missing sequence from reference component AL691432.54 that affects CDC2L1 (GeneID:984) in GRCh37. Navigating to this region in gEVAL and turning on the tracks for:
Upon further review and analysis, the GRC curation team was able to place in to motion new clone sequence to represent correctly this region. The new path is represented in GRCh38 below. The addition of clone FO704657 on to the assembly path correctly contains the complete coding region for the cdc2L1(cdk11b) gene. It also corrects the flanking gene mappings as well. This is indicated by the green mappings of the REFSEQ transcripts. The discordant red features of the Bionano genome maps are no long present, replaced with concordant fragment mappings. The issue can be updated as resolved.
For more information on how to use BioNano displays in gEVAL, check out the gEVAL browser blog.
Comparison of a reference assembly to a collection of whole genome maps can help curators find potential regions of misassembly and identify genomic variations that are candidates for representation in alternate loci scaffolds. For example, optical maps played a key role in the GRC's resolution of the human 10q11.22 tiling path, as described in this prior GRC blog post.
To assist with curation efforts, the Wellcome Trust Sanger Institute, a GRC member, has integrated BioNano data sets for human, mouse and zebrafish assemblies into the gEVAL browser. They have also provided data from OpGen maps and optical maps from David Schwartz (PMID: 20534489). Common curation use cases for these browser data include:
- Gap sizing
- Confirmation of assembly components
- Identification of problems in assembly components
- Identification of assembly regions missing sequence
- Detection of haplotype over-expansions
Below is an example highlighting the potential usage.
The issue (HG-172) reports possible assembly error or missing sequence from reference component AL691432.54 that affects CDC2L1 (GeneID:984) in GRCh37. Navigating to this region in gEVAL and turning on the tracks for:
- REFSEQ transcript mappings
- BspQI insilico digest
- JIRA issue entries
- Bionano genome maps
- NA12878
- NA24143 (Ashkenazim trio mother)
- NA24149 (Ashkenazim trio father)
- NA24385 (Ashkenazim trio son)
- NA24631 (Chinese trio son)
 | ||||
| Jump to this Region in gEVAL |
Zooming into the region of the red features in the Bionano genome maps reveals clearly the fragment sizes between Bionano BspQI nicks/labels. The red features within each map indicates a discordance in size with the BspQI insilico digest.
The insilico digest reveals that the region in question on the assembly has a fragment size of ~26,5kb, whereas all 5 genome maps reveal two fragments totaling ~30kb. This discordant region encompasses the cdc2L1 gene (which from further analysis indicates 2 exons missing) as well, giving evidence that perhaps this region is not represented correctly and missing roughly 3-4kb of sequence.
Upon further review and analysis, the GRC curation team was able to place in to motion new clone sequence to represent correctly this region. The new path is represented in GRCh38 below. The addition of clone FO704657 on to the assembly path correctly contains the complete coding region for the cdc2L1(cdk11b) gene. It also corrects the flanking gene mappings as well. This is indicated by the green mappings of the REFSEQ transcripts. The discordant red features of the Bionano genome maps are no long present, replaced with concordant fragment mappings. The issue can be updated as resolved.
 |
| Jump to this Region in GRCh38 |
For more information on how to use BioNano displays in gEVAL, check out the gEVAL browser blog.
Faked just moved the show dating game women dating sites older to the best dating. Clicked specifically targeted at dating violence of definition thebest dating. Sales way to make the best dating. (Michael Kors Jet Set Black Crossbody Bag)
ReplyDeleteCoach Bags Outlet Online Reviews, LOCAL NEWS ITEMS council is organising a bicycle rental scheme based in the port area. There are a total of 18 bicycles available from Monday to Friday from 11:00am to 11:00pm at for one hour, for four hours and for all day. Malaga city has a similar scheme which is free and more than 17,000 people used it in the first 12 months.
Black And White Stripe Coach Purse, The most savvy businesses crank up their content material anywhere from three to six months before Black Comes to an end. By making sure their website is pumped full of SEO, businesses secure great page rankings before a sluggish start holiday ordering. Many potential customers may search in Google for "coach black friday 2016" and "holiday savings" so make sure your website has these keywords integrated throughout its content.
Are The Bags From Coach Outlet Real, In a statement released Friday afternoon, Meyer admitted he had knowledge of the domestic abuse allegations brought against Zach Smith in 2015 despite claiming otherwise last week, and asserted that he reported the situation in accordance with Ohio State's policies. Meyer, who was placed on paid administrative leave by the university Wednesday, said in the statement that he has "always followed proper reporting protocols and procedures when I have learned of an incident involving a student athlete, coach or member of our staff by elevating the issues to the proper channels. And I did so regarding the Zach Smith incident in 2015.".
Coach Bags Outlet Near Me, Wanted to kill a young boy of 13 years of age. They wanted to kill him. And their interpretation was that he would grow. By World War I, it had been virtually eliminated by cheaper methods. The transfer is lifted onto tissue thin paper from an engraved copper plate that previously has been inked or colored. The paper is then carefully removed, usually by washing or floating it off in water and the lid glazed and fired to fix the design as an integral part of the pottery.. (Michael Kors Black Leather Purse With Gold Chain)