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Variant Discovery and Genome Assembly Melissa Wilson Sayres Prithika Sritharan (Dicks) Zemin Ning (Durbin) Variant Discovery and Genome Assembly Melissa Wilson Sayres Sex Differences in Reference Genome Affect Variant Calling and Differential Expression X and Y homology dotplot a few regions of alignment (PAR) @sexchrlab doi.org/10.1101/346940 https://www.biorxiv.org/content/early/2018/07/18/346940 preprint on correct tech biases on sex chr in NGS data infer sex chromosome complement pointing out regions on autosomes with sex chr - like alignment which is screwing up read balance which presumably could influence variant calling chrY var calls will have many errors

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Day 3 Rafael Irizarry Keynote Session 4: Transcriptomics, Alternative Splicing and Gene Predictions Mark Robinson (Robinson) Hagen Tilgner (Tilgner) Nikka Keivanfar (Church, 10X) Koen Van den Berge (Clement) Barbara Englehardt (Englehardt) Jeff Gaither (White) Fiona Dick (Tzoulis) Epigenetics and non-coding genome Jordana Bell (Bell) Wouter Meuleman (Stamatoyannopoulos) Maša Roller (Flicek) Alexander Suh (Suh) Raquel Garcia-Perez (Juan) Day 3 Very sparse and poorly written notes covering #GI2018.

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Day Two Personal and Medical Genomics Katie Pollard Keynote Sri Kosuri (Kosuri) Patrick Brennan (Nationwide Children’s) Kaitlin Samocha (Hurles) Tracy Ballinger (Semple) Lucia Spangenberg (Naya) Comparative, Evolutionary, Metagenomics Ellen Leffler (Kwiatkowski) Luca Penso-Dolfin (Di Palma) Mario Caccamo (NIAB) Carla Cummins (Flicek) Day Two Personal and Medical Genomics Very sparse and poorly written notes covering #GI2018. Typos everywhere. Things may change dramatically over time as I scan back through notes.

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Intro 2018-09-17 Sarah Teichmann (Teichmann Lab) Girgio Gonnella (Stefan Kurtz) Luke Zappia (Oshlack?) Laura Huerta (Papatheodorou) Casey Greene (Greene) Sergei Yakneen Intro Very sparse and poorly written notes covering #GI2018. Typos everywhere. Things may change dramatically over time as I scan back through notes. I’ve tried to respect #notwitter. Will be updated periodically. Speaker (Lab | Group) BOLDED is voice 2018-09-17 Sarah Teichmann (Teichmann Lab) Cell Atlas Technologies and the Maternal-Fetal Interface

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Background There are several popular naming systems for (human) genes: RefSeq (NM_000350) Ensembl (ENSG00000198691) HGNC Symbol (ABCA4) Entrez (24) Given enough time in #bioinformatics, you will have to do every possible combination of conversions. This post will very briefly explain the most expedient way to automatically convert between these formats with R. More exhaustive resources http://crazyhottommy.blogspot.com/2014/09/converting-gene-ids-using-bioconductor.html https://davetang.org/muse/2013/11/25/thoughts-converting-gene-identifiers/ Ensembl <-> HGNC <-> Entrez Stephen Turner has built a small set of data frames (well, tibbles) with core information, including transcript <-> gene info.

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eyeIntegration

Integration of public human eye RNA-seq datasets https://eyeintegration.nei.nih.gov.

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John Bryan

John Bryan is working on network analysis of large sets of RNA-seq data for the eyeIntegration project