{"id":2707,"date":"2022-12-24T10:59:10","date_gmt":"2022-12-24T16:59:10","guid":{"rendered":"https:\/\/kermitmurray.com\/msblog\/?page_id=2707"},"modified":"2022-12-25T09:56:00","modified_gmt":"2022-12-25T15:56:00","slug":"reddit-r-genomics","status":"publish","type":"page","link":"https:\/\/kermitmurray.com\/msblog\/links\/social-feeds\/reddit-feeds\/reddit-r-genomics\/","title":{"rendered":"Reddit r\/genomics"},"content":{"rendered":"\n<div class=\"wp-block-caxton-grid relative\"><div class=\"absolute absolute--fill\"><div class=\"absolute absolute--fill cover bg-center\" style=\"background-color:;background-image:linear-gradient( );\"><\/div><div class=\"absolute absolute--fill\" style=\"background-color:;background-image:linear-gradient( );opacity:1;\"><\/div><\/div><div class=\"relative caxton-columns caxton-grid-block\" style=\"padding-top:0;padding-left:0;padding-bottom:0;padding-right:0;grid-template-columns:repeat(12, 1fr)\" data-tablet-css=\"padding-left:em;padding-right:em;\" data-mobile-css=\"padding-left:em;padding-right:em;\">\n<div class=\"wp-block-caxton-section relative\" style=\"grid-area:span 1\/span 8\"><div class=\"absolute absolute--fill\"><div class=\"absolute absolute--fill cover bg-center\" style=\"background-color:;background-image:linear-gradient( );\"><\/div><div class=\"absolute absolute--fill\" style=\"background-color:;background-image:linear-gradient( );opacity:1;\"><\/div><\/div><div class=\"relative caxton-section-block\" style=\"padding-top:5px;padding-left:5px;padding-bottom:5px;padding-right:5px\" data-mobile-css=\"padding-left:1em;padding-right:1em;\" data-tablet-css=\"padding-left:1em;padding-right:1em;\">\n<p><a href=\"https:\/\/www.reddit.com\/r\/genomics\/\" target=\"_blank\" rel=\"noreferrer noopener\"><strong>\/r\/genomics\/<\/strong><\/a><\/p>\n<\/div><\/div>\n\n\n\n<div class=\"wp-block-caxton-section relative\" style=\"grid-area:span 1\/span 4\"><div class=\"absolute absolute--fill\"><div class=\"absolute absolute--fill cover bg-center\" style=\"background-color:;background-image:linear-gradient( );\"><\/div><div class=\"absolute absolute--fill\" style=\"background-color:;background-image:linear-gradient( );opacity:1;\"><\/div><\/div><div class=\"relative caxton-section-block\" style=\"padding-top:5px;padding-left:5px;padding-bottom:5px;padding-right:5px\" data-mobile-css=\"padding-left:1em;padding-right:1em;\" data-tablet-css=\"padding-left:1em;padding-right:1em;\">\n<p><strong><a href=\"https:\/\/www.reddit.com\/r\/genomics.rss\" target=\"_blank\" rel=\"noreferrer noopener\">RSS<\/a><\/strong><\/p>\n<\/div><\/div>\n<\/div><\/div>\n\n\n<ul class=\"has-dates has-authors has-excerpts wp-block-rss\"><li class='wp-block-rss__item'><div class='wp-block-rss__item-title'><a href='https:\/\/www.reddit.com\/r\/genomics\/comments\/1srsjfk\/fastvep_rustbased_vep_that_annotates_4m_wgs\/'>fastVEP: Rust-based VEP that annotates 4m WGS variants in 1.5 minutes (130x faster than VEP, Open Source)<\/a><\/div><time datetime=\"2026-04-21T16:19:15-05:00\" class=\"wp-block-rss__item-publish-date\">April 21, 2026<\/time> <span class=\"wp-block-rss__item-author\">by \/u\/Spiritual-Feed-3296<\/span><div class=\"wp-block-rss__item-excerpt\">I rewrote Ensembl VEP in Rust. It&#039;s 130x faster. https:\/\/fastvep.org\/ Got tired of waiting hours for VEP during my PhD, so I eventually just&#8230; rebuilt the whole thing (thanks to agentic coding). fastVEP annotates 4M+ WGS variants (full GIAB HG002, 508K transcripts) in about 1.5 minutes on my MacBook. Ensembl VEP can&#039;t finish that run on my notebook. On smaller subsets where both tools finish, fastVEP is 130x faster. Accuracy: 100% match across 23 fields on 2,340 transcript-allele pairs vs. VEP v115.1. I didn&#039;t cut corners \u2014 same GFF3, same FASTA, same flags. What&#039;s in it: &#8211; 49 SO terms, [&hellip;]<\/div><\/li><li class='wp-block-rss__item'><div class='wp-block-rss__item-title'><a href='https:\/\/www.reddit.com\/r\/genomics\/comments\/1sqtw33\/rnaseq_analysis_series_complete_3part_tutorial\/'>RNA-seq Analysis Series \u2014 Complete 3-Part Tutorial (Workflow, Alignment &amp; DESeq2)<\/a><\/div><time datetime=\"2026-04-20T16:12:14-05:00\" class=\"wp-block-rss__item-publish-date\">April 20, 2026<\/time> <span class=\"wp-block-rss__item-author\">by \/u\/rikkibioinfo<\/span><div class=\"wp-block-rss__item-excerpt\">A 3-part hands-on RNA-seq tutorial series by Dr. Babajan Banaganapali (Bioinformatics With BB), covering the complete pipeline from raw reads to DESeq2 normalization and visualization. Part 1 \u2014 Introduction &amp; Workflow (RNA-seq types, wet-lab steps, full pipeline overview) https:\/\/youtu.be\/dq31baC_AHs Part 2 \u2014 QC, Alignment &amp; Quantification (FastQC, Cutadapt, STAR\/HISAT2, FeatureCounts \u2014 with real troubleshooting) https:\/\/youtu.be\/4y2R2PgdBHo Part 3 \u2014 DESeq2 Normalization, Visualization &amp; Interpretation (R, size-factor normalization, heatmaps, expression plots) https:\/\/www.youtube.com\/watch?v=DxesV0eWtTQ Reproducible R and bash scripts are linked in each video description. submitted by \/u\/rikkibioinfo [link] [comments]<\/div><\/li><li class='wp-block-rss__item'><div class='wp-block-rss__item-title'><a href='https:\/\/www.reddit.com\/r\/genomics\/comments\/1soqoyk\/i_named_my_aws_finalist_project_anukriti_sanskrit\/'>I named my AWS finalist project &quot;Anukriti&quot; \u2014 Sanskrit for reaction\/response. It&#039;s a genomic drug safety tool built because Indian and Global South labs keep getting excluded from pharmaceutical research. Need your support.<\/a><\/div><time datetime=\"2026-04-18T07:14:30-05:00\" class=\"wp-block-rss__item-publish-date\">April 18, 2026<\/time> <span class=\"wp-block-rss__item-author\">by \/u\/Poseidonmagma<\/span><div class=\"wp-block-rss__item-excerpt\">Something that doesn&#039;t get talked about enough: 83.8% of global drug safety genomic research comes from European populations. When a drug gets approved, the safety evidence is almost entirely built on European genomes \u2014 then it&#039;s prescribed in India, Africa, East Asia, without adjustment. The consequences are real: Carbamazepine causes Stevens-Johnson Syndrome almost exclusively in carriers of HLA-B*15:02 \u2014 present in ~10% of Han Chinese, virtually absent in Europeans. European-majority Phase III trials never caught this. Clopidogrel fails as a prodrug in 57% of Pacific Islanders due to a metabolizer gene variant. Standard warfarin doses cause bleeding in East Asian [&hellip;]<\/div><\/li><li class='wp-block-rss__item'><div class='wp-block-rss__item-title'><a href='https:\/\/www.reddit.com\/r\/genomics\/comments\/1sodzhc\/paxgene_rna_tubes\/'>PAXgene RNA tubes?<\/a><\/div><time datetime=\"2026-04-17T21:19:46-05:00\" class=\"wp-block-rss__item-publish-date\">April 17, 2026<\/time> <span class=\"wp-block-rss__item-author\">by \/u\/Regular_Tailor<\/span><div class=\"wp-block-rss__item-excerpt\">Hey researchers or disgruntled lab managers! I&#039;m a human trying to do an N of One study on a promising gene silencing hypothesis. We&#039;re trying to get 5-6 PAXgene tubes for collection. We don&#039;t have any institutional affiliation and we&#039;re 100% down to cover costs, but a pack of 100 is straining our household budget. Any help appreciated, DM with leads! submitted by \/u\/Regular_Tailor [link] [comments]<\/div><\/li><li class='wp-block-rss__item'><div class='wp-block-rss__item-title'><a href='https:\/\/www.reddit.com\/r\/genomics\/comments\/1sn558a\/the_new_moderator_of_rgenomics_must_go\/'>The new moderator of r\/genomics must go<\/a><\/div><time datetime=\"2026-04-16T14:27:52-05:00\" class=\"wp-block-rss__item-publish-date\">April 16, 2026<\/time> <span class=\"wp-block-rss__item-author\">by \/u\/bioinfoAgent<\/span><div class=\"wp-block-rss__item-excerpt\">Yesterday, the new moderator flagged three of my replies as \u201cbreaks the be-kind rule\u201d and overlooked other unfriendly replies to my post. This was all done because the MOD hates AI, and that was the main message of my post. Subjective decision destroy Reddit\u2019s user experience. We must all ask Reddit to revoke this woke (meaning irrational, detached from reality) moderator and make [r\/genomics](r\/genomics) a place of unbiased scientific discourse. submitted by \/u\/bioinfoAgent [link] [comments]<\/div><\/li><li class='wp-block-rss__item'><div class='wp-block-rss__item-title'><a href='https:\/\/www.reddit.com\/r\/genomics\/comments\/1smu1wm\/covsnap_a_simple_coverage_qc_tool_for_targeted\/'>covsnap &#8211; a simple coverage QC tool for targeted sequencing (hg38, single command, interactive HTML report)<\/a><\/div><time datetime=\"2026-04-16T05:09:46-05:00\" class=\"wp-block-rss__item-publish-date\">April 16, 2026<\/time> <span class=\"wp-block-rss__item-author\">by \/u\/akenes96<\/span><div class=\"wp-block-rss__item-excerpt\">submitted by \/u\/akenes96 [link] [comments]<\/div><\/li><li class='wp-block-rss__item'><div class='wp-block-rss__item-title'><a href='https:\/\/www.reddit.com\/r\/genomics\/comments\/1smo3yn\/varcrawl_free_opensource_web_tool_to_search_for_a\/'>VarCrawl: Free Open-Source Web Tool to search for a Mutation\/Variant on every name it goes by<\/a><\/div><time datetime=\"2026-04-16T00:33:17-05:00\" class=\"wp-block-rss__item-publish-date\">April 16, 2026<\/time> <span class=\"wp-block-rss__item-author\">by \/u\/Spiritual-Feed-3296<\/span><div class=\"wp-block-rss__item-excerpt\">Try it here: https:\/\/var-crawl.vercel.app\/ https:\/\/github.com\/Huang-lab\/VarCrawl I don&#039;t think there&#039;s a need to publish this so want to promote here for people to use it, please help spread the word to whoever finds this helpful! submitted by \/u\/Spiritual-Feed-3296 [link] [comments]<\/div><\/li><li class='wp-block-rss__item'><div class='wp-block-rss__item-title'><a href='https:\/\/www.reddit.com\/r\/genomics\/comments\/1smc8d6\/ancient_dna_reveals_pervasive_directional\/'>Ancient DNA reveals pervasive directional selection across West Eurasia (Published in Nature)<\/a><\/div><time datetime=\"2026-04-15T17:08:47-05:00\" class=\"wp-block-rss__item-publish-date\">April 15, 2026<\/time> <span class=\"wp-block-rss__item-author\">by \/u\/Holodoxa<\/span><div class=\"wp-block-rss__item-excerpt\">submitted by \/u\/Holodoxa [link] [comments]<\/div><\/li><li class='wp-block-rss__item'><div class='wp-block-rss__item-title'><a href='https:\/\/www.reddit.com\/r\/genomics\/comments\/1smc6v2\/multiancestry_genomewide_association_study_of\/'>Multi-ancestry genome-wide association study of severe pregnancy nausea and vomiting<\/a><\/div><time datetime=\"2026-04-15T17:07:17-05:00\" class=\"wp-block-rss__item-publish-date\">April 15, 2026<\/time> <span class=\"wp-block-rss__item-author\">by \/u\/Holodoxa<\/span><div class=\"wp-block-rss__item-excerpt\">submitted by \/u\/Holodoxa [link] [comments]<\/div><\/li><li class='wp-block-rss__item'><div class='wp-block-rss__item-title'><a href='https:\/\/www.reddit.com\/r\/genomics\/comments\/1slvz1p\/i_built_an_agent_that_runs_scrnaseq_workflows_via\/'>I built an agent that runs scRNA-seq workflows via natural language \u2014 tested on SC-Bench<\/a><\/div><time datetime=\"2026-04-15T04:37:44-05:00\" class=\"wp-block-rss__item-publish-date\">April 15, 2026<\/time> <span class=\"wp-block-rss__item-author\">by \/u\/thewall888<\/span><div class=\"wp-block-rss__item-excerpt\">scAgent I\u2019ve been working on an AI agent (scAgent) that can run end-to-end scRNA-seq analysis through natural language, and wanted to share it here for feedback from people who actually work with this data. The goal wasn\u2019t just \u201cchat with your data,\u201d but something that can reliably execute real workflows \u2014 including handling partially processed datasets, tracking decisions, and staying reproducible. What it does in practice: Runs full pipelines: QC \u2192 normalization \u2192 HVG \u2192 PCA \u2192 batch correction \u2192 clustering \u2192 annotation (CellTypist) \u2192 DE (pseudobulk via DESeq2 \/ edgeR) \u2192 GSEA Accepts raw Cell Ranger output or .h5ad [&hellip;]<\/div><\/li><li class='wp-block-rss__item'><div class='wp-block-rss__item-title'><a href='https:\/\/www.reddit.com\/r\/genomics\/comments\/1slmams\/pitfalls_in_estimating_and_interpreting_the\/'>Pitfalls in estimating and interpreting the contribution of ultra-rare genetic variants to the heritability of complex traits<\/a><\/div><time datetime=\"2026-04-14T21:33:01-05:00\" class=\"wp-block-rss__item-publish-date\">April 14, 2026<\/time> <span class=\"wp-block-rss__item-author\">by \/u\/Holodoxa<\/span><div class=\"wp-block-rss__item-excerpt\">submitted by \/u\/Holodoxa [link] [comments]<\/div><\/li><li class='wp-block-rss__item'><div class='wp-block-rss__item-title'><a href='https:\/\/www.reddit.com\/r\/genomics\/comments\/1skwl5l\/we_created_an_opensource_knowledge_graph_of\/'>We created an open-source knowledge graph of bioinformatics workflows extracted from 20K+ papers, available as an MCP server<\/a><\/div><time datetime=\"2026-04-14T03:01:57-05:00\" class=\"wp-block-rss__item-publish-date\">April 14, 2026<\/time> <span class=\"wp-block-rss__item-author\">by \/u\/bioinfoAgent<\/span><div class=\"wp-block-rss__item-excerpt\">https:\/\/preview.redd.it\/ax9gsiqbn2vg1.png?width=3354&amp;format=png&amp;auto=webp&amp;s=f14f4cc2afa326523a980388931f03d6e860710c I&#039;ve been in bioinformatics for 20+ years and have been working on agentic pipelines for the past year. Ran into a problem that I think anyone using Claude Code or Codex for bioinformatics work has hit: The agent can write the code. It doesn&#039;t know the field. It&#039;ll chain tools together in an order that&#039;s plausible but not standard. Skip QC steps. Pick defaults that are technically valid but wrong for the data type. No provenance for any of it. Community-standard workflows live in papers and practitioner intuition, not in model weights. So I built Skill Graph. It&#039;s a [&hellip;]<\/div><\/li><\/ul>\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity is-style-wide\"\/>\n\n\n\n<h4 class=\"wp-block-heading\">Related Feeds<\/h4>\n\n\n<ul class=\"su-siblings\"><li class=\"page_item page-item-2733\"><a href=\"https:\/\/kermitmurray.com\/msblog\/links\/social-feeds\/reddit-feeds\/reddit-r-analyticalchemistry\/\">Reddit r\/analyticalchemistry<\/a><\/li>\n<li class=\"page_item page-item-2473\"><a href=\"https:\/\/kermitmurray.com\/msblog\/links\/social-feeds\/reddit-feeds\/reddit-r-massspectrometry\/\">Reddit r\/massspectrometry<\/a><\/li>\n<li class=\"page_item page-item-2705\"><a href=\"https:\/\/kermitmurray.com\/msblog\/links\/social-feeds\/reddit-feeds\/reddit-r-metabolomics\/\">Reddit r\/metabolomics<\/a><\/li>\n<li class=\"page_item page-item-2499\"><a href=\"https:\/\/kermitmurray.com\/msblog\/links\/social-feeds\/reddit-feeds\/reddit-r-proteomics\/\">Reddit r\/proteomics<\/a><\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Related Feeds<\/p>\n","protected":false},"author":1,"featured_media":2498,"parent":2738,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":"","_links_to":"","_links_to_target":""},"class_list":["post-2707","page","type-page","status-publish","has-post-thumbnail","hentry","entry"],"_links":{"self":[{"href":"https:\/\/kermitmurray.com\/msblog\/wp-json\/wp\/v2\/pages\/2707","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/kermitmurray.com\/msblog\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/kermitmurray.com\/msblog\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/kermitmurray.com\/msblog\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/kermitmurray.com\/msblog\/wp-json\/wp\/v2\/comments?post=2707"}],"version-history":[{"count":2,"href":"https:\/\/kermitmurray.com\/msblog\/wp-json\/wp\/v2\/pages\/2707\/revisions"}],"predecessor-version":[{"id":2746,"href":"https:\/\/kermitmurray.com\/msblog\/wp-json\/wp\/v2\/pages\/2707\/revisions\/2746"}],"up":[{"embeddable":true,"href":"https:\/\/kermitmurray.com\/msblog\/wp-json\/wp\/v2\/pages\/2738"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/kermitmurray.com\/msblog\/wp-json\/wp\/v2\/media\/2498"}],"wp:attachment":[{"href":"https:\/\/kermitmurray.com\/msblog\/wp-json\/wp\/v2\/media?parent=2707"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}