498 results • Page 1 of 17
The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed... go to blog
Just realised that other than vcf-compare and bedtools intersect there's other options https://github.com/RealTimeGenomics/rtg-toolshttps://github.com/Illumina/hap.py Also there's actually new variant callers .. Molina-Mora, J.A., Solano-Vargas, M. Set-theory based benchmarking of three different variant callers for targeted sequencing. BMC Bioinformatics 22, 20 (2021). https://doi.org/10.1186/s12859-020-03926-3 Krishnan, V., Utiramerur, S., Ng, Z. et al. Benchmarking workflows to assess performance and suitability of germline variant calling pipelines in clinical diagnostic assays. BMC Bioinformatics 22, 85 (2021). https://doi.org/10.1186/s12859-020-03934-3Additional file 23: File 3. verify_variants.py Zook, Justin M et … go to blog
The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed... go to blog
If you have had to upload omics data to GEO before, you'll know it's a bit of a hassle and takes a long time. There are a few methods suggested by the GEO team if you are using the Unix command line: Using 'ncftp'ncftpset passive onset so-bufsize 33554432open ftp://geoftp:yourpasscode@ftp-private.ncbi.nlm.nih.govcd uploads/your@mail.com_yourfolderput -R Folder_with_submission_filesUsing 'lftp'lftp ftp://geoftp:yourpasscode@ftp-private.ncbi.nlm.nih.govcd uploads/your@mail.com_yourfoldermirror -R Folder_with_submission_filesUsing 'sftp' (expect slower transfer speeds since this method encrypts on-the-fly)sftp geoftp@sftp-private.ncbi.nlm.nih.govpassword: yourpasscodecd uploads/your@mail.com_yourfoldermkdir new_geo_submissioncd new_geo_submissionput file_nameUsing 'ncftpput' (transfers from the command-line without entering … go to blog
So our preprint is online called “Guidelines for reliable and reproducible functional enrichment analysis” so I thought I’d give you an overview.Enrichment analysis is widely used for exploration and interpretation of omics data, but I’ve noticed sloppy work is becoming more common. Over the past few years I’ve been asked to review several manuscripts where the enrichment analysis was poorly conducted and reported. Examples of this include lack of FDR control, incorrect background gene list specification and lack of essential … go to blog
The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed... go to blog
The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed... go to blog
The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed... go to blog
(a) 1616: A movement or change of position, e.g., “The nature of this Euolution is clearely to leaue the File-leaders in front, and Bringers in reare.”(b) 1624: The process of unrolling, opening out, or revealing.© 1671: The process by which living organisms or their parts develop from a rudimentary to a mature or complete state. These days, this process is referred to as “development.” The first use of “evolution” in this sense appears in an anonymous book review published in … go to blog
A letter from the President of University of Houston, Renu Khator, landed in my inbox on August 10 at 1:00 PM. I was waiting for such a letter to see how a responsible university president will deal with the inane rules of Texas governor, Greg Abbott, who decreed that public schools are require marks, proof of vaccination, testing, or social distancing. I was also looking—most probably naively—at some signs of civic responsibility, of putting the interests of her “subjects” above … go to blog
The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed... go to blog
I was on vacation early this week when the news broke that PacBio has acquired HMW DNA solid phase extraction kit maker Circulomics -- the kind of vacation that I need where the scenery is gorgeous and the internet access terrible. Where solid phase means monumental slabs of granite with diabase intrusions being attacked by a high salt liquid phase. Where I actually sighted Atlantic Puffins and didn't once think about sequencing their genomes ('til now!). But now I'm back … go to blog
The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed... go to blog
It’s an old favourite of this blog, isn’t it. We had Gene name errors and Excel: lessons not learned (2012). Followed by Data corruption using Excel: 12+ years and counting (2016). Perhaps most depressingly of all, the conclusion of the trilogy, When your tools are broken, just change the data (2019-20). Well, I’m happy (?) … Continue reading Gene names, data corruption and Excel: a 2021 update go to blog
Our latest article "Gene name errors: Lessons not learned" previously @biorxiv_genomic has just been published in PLoS Computational Biology (link here). In this post I'll walk you through why it is so important to how computational biology is done. If you are a regular GenomeSpot reader you are probably well aware about how Excel mangles gene names. So why the need for a 2021 update? Well we thought that the broader genomics community would know about it by now. It … go to blog
The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed... go to blog
The first patch release for the GRCh38 reference assembly is now available. The GRCh38.p1 release includes 16 scaffolds: 13 FIX patches and 3 NOVEL patches. The FIX patch scaffolds correct existing assembly sequences, while the NOVEL patch scaffolds provide new alternate sequence representations. You can download the GRCh38.p1 assembly, including the alignments of the patches to GRCh38, from the GenBank FTP site: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000001405.16_GRCh38.p1/.Stay tuned for upcoming blog posts on individual patches! go to blog
The GRC are now providing assembly-related tracks for reference genomes via a track hub, which will allow you to view that data in a range of genome browsers, including Ensembl and UCSC. The location of this hub is: http://ngs.sanger.ac.uk/production/grit/track_hub/hub.txtWhat tracks are available?The GRC generates a range of annotations on the reference genomes it curates. These tracks describe the assembly of the genome, as well as quality issues with the genome, and provides information relevant to their resolution or planned improvement. … go to blog
The GRC track hub now includes Optical Mapping analysis information.What is Optical Mapping? Optical Mapping (OM) is a method to produce ordered restriction maps from single DNA molecules (rMaps). These rMaps are assembled into consensus maps which can be aligned against the reference assembly, taking into account the positioning of restriction sites and length of fragments. OM aids the scaffolding of genomic sequence and the identification of errors in genome assemblies, but it is also very helpful in confirming assembled … go to blog
GRCh38 has started receiving patch updates, and this blog post describes a FIX patch to the ABO gene, located on chr. 9. You might have been aware that the GRC released a FIX patch to ABO for GRCh37. So why is there an ABO FIX patch for GRCh38 as well?In GRCh37, the ABO gene was annotated on sequence derived from two RP11 library clones, AL732364.9 (RP11-244N20) and AL158826.23 (RP11-430N14). However, the RP11 library is derived from a diploid genome and … go to blog
I’ve long admired the look of publications generated using the R bookdown package, and thought it would be fun and educational to publish one myself. The problem is that I am not writing a book and have no plans to do so any time soon. Then I remembered that I’ve already written a book. There … Continue reading How I resurrected my ancient PhD thesis using R/bookdown (and some other tools) go to blog
GRC "Genome Issues under Review" webpage update!Do you know how to find genome issues on the GRC website? To get started, select an organism from the top of the GRC homepage, and in the corresponding organism overview page select the link for "Issues Under Review". These pages provide you with the latest information about potential problems and other issues related to the human, mouse and zebrafish reference genome assemblies that the GRC are working on. Recent updates to these pages … go to blog
Are you looking for the latest status updates from the GRC on the human, mouse or zebrafish reference genome assemblies? In companion to our previous post, we now explain how to use the Individual Genome Issue reports on the GRC website. As described in our last blog, you can filter and search for issues of interest using the organism-specific "Issues Under Review" pages. To provide an example for this blog post, we applied the follow filtering options on the human … go to blog
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 … go to blog
Sequence improvements and increased variant representation in the human genome reference assembly are priorities for the GRC. This blog post describes two updates in the recent GRCh38.p7 patch release affecting the DUX4 region located at the chromosome 4q sub-telomere: (1) a FIX patch correcting the chromosomal representation (KQ983257.1) and (2) a NOVEL patch representing a variant of the region (KQ983258.1). A third haplotype of DUX4 region which is represented in GRCh37 will be also described.The DUX4 region contains tandem arrays … go to blog
Upon the release of Gallus_gallus-5.0 (GCA_000002315.3), the GRC assumed responsibility for the continued curation of the chicken reference genome assembly from the International Chicken Genome Consortium. The assembly represents the Red Jungle Fowl strain, inbred line UCD001. All sequences in the assembly are derived from a single individual from this line, female "RJF #256". The assembly is a hybrid comprised primarily of WGS contigs, into which genomic clones have been integrated. Planned curation efforts are focused on selecting genomic clones … go to blog
ZFIN, the zebrafish model organism database, is joining the GRC and is planning to take over the maintenance and curation of the zebrafish genome assembly. ZFIN curators visited with GRC curators at the Wellcome Trust Sanger Institute in January 2016 to undergo training in the use of GRC tools and processes. ZFIN anticipates taking over responsibility after the next planned release of the zebrafish assembly, GRCz11. A specific timeline for this release has not yet been established, but is likely … go to blog
CYP2D6 (Gene ID: 1565) is a gene associated with the metabolism of ~25% of clinically prescribed drugs, including antidepressants, neuroleptics and opioids. CYP2D6 is located on chromosome 22 (22q13.1), near two cytochrome P450 pseudogenes CYP2D7 and CYP2D8P. Because of its functional importance, the GRC updated the chromosomal representation for CYP2D6 to the sequence-corrected clinical standard (CYP2D6*1A) in GRCh38. The version of CYP2D6 found in the prior assembly version, GRCh37, was retained in GRCh38 as an alternate loci scaffold (KI270928.1).The Genome … go to blog
The KIR (Killer cell immunoglobulin-like receptor) gene cluster is a region of approximately 150 kb within the Leukocyte Receptor Complex (LRC) on human chromosome 19q13.4 (CM000681.2: 50900001-58617616). The KIR family is highly divergent, with multiple haplotypes differing in gene content, and with individual genes exhibiting allelic variation. Only a few KIR genes are conserved between humans and chimpanzees, the closest living relatives to humans. The GRCh38 assembly includes 35 representations for the LRC-KIR region as alternate loci scaffolds in addition … go to blog
498 results • Page 1 of 17
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