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nf-corePipeline release! nf-core/rnavar v1.1.0 - nf-core/rnavar 1.1.0 - Mighty Milano!Please see the changelog: <a href="https://github.com/nf-core/rnavar/releases/tag/1.1.0" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://github.com/nf-core/rnavar/releases/tag/1.1.0</a><a href="https://mstdn.science/tags/gatk4" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#gatk4</a> <a href="https://mstdn.science/tags/rna" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#rna</a> <a href="https://mstdn.science/tags/rnaseq" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#rnaseq</a> <a href="https://mstdn.science/tags/variantcalling" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#variantcalling</a> <a href="https://mstdn.science/tags/worflow" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#worflow</a> <a href="https://mstdn.science/tags/nfcore" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#nfcore</a> <a href="https://mstdn.science/tags/openscience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#openscience</a> <a href="https://mstdn.science/tags/nextflow" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#nextflow</a> <a href="https://mstdn.science/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bioinformatics</a>

Pierre Lindenbaumasking for a friend: do you know any database/framework to visualize RNAseq data ? (just like <a href="https://github.com/broadinstitute/gnomad-browser" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://github.com/broadinstitute/gnomad-browser</a> for WGS)<a href="https://genomic.social/tags/database" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#database</a> <a href="https://genomic.social/tags/rnaseq" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#rnaseq</a> <a href="https://genomic.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bioinformatics</a>

(((@amarois)))Plaisir du samedi de perm à la BU: lecture de <a href="https://mamot.fr/tags/PGD" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#PGD</a> "L. Gress, S. Maman-Haddad, N. Marty-Gasset, N. Vialaneix, A. Bonnet. Plan de gestion des données CO-LOcATION V. Finale. INRAE-UMR GenPhySE 2025 <a href="https://hal.inrae.fr/hal-05009536v1" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://hal.inrae.fr/hal-05009536v1</a> <a href="https://mamot.fr/tags/passionPGD" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#passionPGD</a> <a href="https://mamot.fr/tags/DMPporn" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#DMPporn</a> <a href="https://mamot.fr/tags/researchdata" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#researchdata</a> <a href="https://mamot.fr/tags/openscience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#openscience</a> <a href="https://mamot.fr/tags/DMP" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#DMP</a> <a href="https://mamot.fr/tags/RNAseq" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#RNAseq</a> <a href="https://mamot.fr/tags/biology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#biology</a> <a href="https://mamot.fr/tags/data" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#data</a>

Bioconductor🌍 Bioconductor Course, Kenya 2025 🎓We’re thrilled to announce our first in-person Bioconductor course in Kenya, happening March 24–28, 2025, at the ILRI Campus in Nairobi!This free, week-long course is for bioinformatics beginners, covering R, Bioconductor, and RNA-seq workflows, and aims to grow the Bioconductor community in Africa.🔗 Apply now: <a href="https://buff.ly/40CJL02" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://buff.ly/40CJL02</a> 🔗 Learn more: <a href="https://training.bioconductor.org/workshops/2025-03-Nairobi/index.html" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://training.bioconductor.org/workshops/2025-03-Nairobi/index.html</a> <a href="https://genomic.social/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Bioinformatics</a> <a href="https://genomic.social/tags/Carpentries" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Carpentries</a> <a href="https://genomic.social/tags/RStats" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#RStats</a> <a href="https://genomic.social/tags/RNAseq" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#RNAseq</a>

Marc Robinson-RechaviWe obtained <a href="https://ecoevo.social/tags/RNAseq" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#RNAseq</a> from tooth germs over the embryonic and postnatal period where the major events of morphogenesis occur, from bud, to cap, to bell stage until differentiation and enamel/dentin secretion, and obtained clusters of coexpressed genes per stage.

victorjavierloLooking for advice on FDR thresholds in <a href="https://genomic.social/tags/GSEA" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#GSEA</a>: Do you typically use FDR < 0.25 or FDR < 0.05 to determine significance? How does your threshold choice change depending on permutation_type='phenotype' vs. permutation_type='gene_set'? <a href="https://genomic.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bioinformatics</a> <a href="https://genomic.social/tags/rnaseq" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#rnaseq</a>

nf-corePipeline release! nf-core/rnaseq v3.16.1 - nf-core/rnaseq v3.16.0 - Further Fire Ferret!Please see the changelog: <a href="https://github.com/nf-core/rnaseq/releases/tag/3.16.1" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://github.com/nf-core/rnaseq/releases/tag/3.16.1</a><a href="https://mstdn.science/tags/rna" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#rna</a> <a href="https://mstdn.science/tags/rnaseq" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#rnaseq</a> <a href="https://mstdn.science/tags/nfcore" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#nfcore</a> <a href="https://mstdn.science/tags/openscience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#openscience</a> <a href="https://mstdn.science/tags/nextflow" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#nextflow</a> <a href="https://mstdn.science/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bioinformatics</a>

Luca VisentinI've yet again been saved by x.FASTQ when realigning GEO/ENA seq data, so I wanted to leave a link to the tool here:<a href="https://github.com/TCP-Lab/x.FASTQ" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://github.com/TCP-Lab/x.FASTQ</a>It's mostly the work of my PI, although I've contributed `metaharvest` to the mix.If you ever need to re-align some GEO samples and have some remote machine to do it in (we use a NUC in the lab), give them a try!`metaharvest` is also nice as it deals with the terrible GEO metadata for you, pooping out a simple `.csv`<a href="https://genomic.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bioinformatics</a> <a href="https://genomic.social/tags/RNAseq" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#RNAseq</a>

Bgee databaseDo you know gget by the Pachter lab? You should! It now includes efficient querying of Bgee in Python. Get high quality curated gene expression data directly in Python or command line. <a href="https://pachterlab.github.io/gget/en/bgee.html" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://pachterlab.github.io/gget/en/bgee.html</a> <a href="https://genomic.social/tags/RNAseq" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#RNAseq</a> <a href="https://genomic.social/tags/biocuration" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#biocuration</a> <a href="https://genomic.social/tags/Python" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Python</a> <a href="https://genomic.social/tags/scRNAseq" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#scRNAseq</a> <a href="https://mstdn.science/@SIB" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@SIB</a> <a href="https://ecoevo.social/@marcrr" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@marcrr</a> <a href="https://ecoevo.social/@fbastian" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@fbastian</a> <a href="https://ecoevo.social/@dee_unil" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@dee_unil</a><a href="https://genomic.social/tags/bgee" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bgee</a> <a href="https://genomic.social/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Bioinformatics</a> <a href="https://genomic.social/tags/RNASequencing" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#RNASequencing</a> <a href="https://genomic.social/tags/SingleCellRNASeq" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#SingleCellRNASeq</a> <a href="https://genomic.social/tags/Genomics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Genomics</a> <a href="https://genomic.social/tags/Transcriptomics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Transcriptomics</a> <a href="https://genomic.social/tags/GeneExpression" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#GeneExpression</a> <a href="https://genomic.social/tags/ComputationalBiology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#ComputationalBiology</a> <a href="https://genomic.social/tags/SingleCellAnalysis" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#SingleCellAnalysis</a> <a href="https://genomic.social/tags/GeneExpressionAnalysis" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#GeneExpressionAnalysis</a>

jobRxivPhD position - Cardiovascular/Cardiometabolic Immunology Ludwig Maximilians University HospitalSee the full job description on jobRxiv: <a href="https://jobrxiv.org/job/ludwig-maximilians-university-hospital-27778-phd-position-cardiovascular-cardiometabolic-immunology-2/?feed_id=82599" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://jobrxiv.org/job/ludwig-maximilians-university-hospital-27778-phd-position-cardiovascular-cardiometabolic-immunology-2/?feed_id=82599</a><a href="https://mas.to/tags/flow_cytometry" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#flow_cytometry</a> <a href="https://mas.to/tags/Heart" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Heart</a> <a href="https://mas.to/tags/macrophage" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#macrophage</a> <a href="https://mas.to/tags/metabolism" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#metabolism</a> <a href="https://mas.to/tags/RNAseq" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#RNAseq</a> <a href="https://mas.to/tags/ScienceJobs" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#ScienceJobs</a> <a href="https://mas.to/tags/hirin" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#hirin</a>... <a href="https://jobrxiv.org/job/ludwig-maximilians-university-hospital-27778-phd-position-cardiovascular-cardiometabolic-immunology-2/?feed_id=82599" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://jobrxiv.org/job/ludwig-maximilians-university-hospital-27778-phd-position-cardiovascular-cardiometabolic-immunology-2/?feed_id=82599</a>

jobRxivPhD position - Cardiovascular/Cardiometabolic Immunology Ludwig Maximilians University HospitalSee the full job description on jobRxiv: <a href="https://jobrxiv.org/job/ludwig-maximilians-university-hospital-27778-phd-position-cardiovascular-cardiometabolic-immunology-2/?feed_id=82529" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://jobrxiv.org/job/ludwig-maximilians-university-hospital-27778-phd-position-cardiovascular-cardiometabolic-immunology-2/?feed_id=82529</a><a href="https://mas.to/tags/flow_cytometry" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#flow_cytometry</a> <a href="https://mas.to/tags/Heart" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Heart</a> <a href="https://mas.to/tags/macrophage" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#macrophage</a> <a href="https://mas.to/tags/metabolism" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#metabolism</a> <a href="https://mas.to/tags/RNAseq" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#RNAseq</a> <a href="https://mas.to/tags/ScienceJobs" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#ScienceJobs</a> <a href="https://mas.to/tags/hirin" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#hirin</a>... <a href="https://jobrxiv.org/job/ludwig-maximilians-university-hospital-27778-phd-position-cardiovascular-cardiometabolic-immunology-2/?feed_id=82529" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://jobrxiv.org/job/ludwig-maximilians-university-hospital-27778-phd-position-cardiovascular-cardiometabolic-immunology-2/?feed_id=82529</a>

Albert Cardona"Whole-embryo Spatial Transcriptomics at Subcellular Resolution from Gastrulation to Organogenesis", by Wan et al. 2024 <a href="https://www.biorxiv.org/content/10.1101/2024.08.27.609868v1" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://www.biorxiv.org/content/10.1101/2024.08.27.609868v1</a><a href="https://mathstodon.xyz/tags/zebrafish" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#zebrafish</a> <a href="https://mathstodon.xyz/tags/RNAseq" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#RNAseq</a> <a href="https://mathstodon.xyz/tags/transcriptomics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#transcriptomics</a> <a href="https://mathstodon.xyz/tags/DevBio" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#DevBio</a> <a href="https://mathstodon.xyz/tags/weMERFISH" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#weMERFISH</a>

Arjan BoltjesThis morning is The Psychotic Monks-morning, the Paris-based outfit and best band playing last Saturday's Loose Ends festival, here in <a href="https://mastodon.social/tags/Utrecht" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Utrecht</a><a href="https://mastodon.social/tags/PlayingNow" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#PlayingNow</a>, their most recent album Pink Colour Surgery out on <a href="https://mastodon.social/tags/FatCat" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#FatCat</a>: <a href="https://fatcatrecords.bandcamp.com/album/pink-colour-surgery" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://fatcatrecords.bandcamp.com/album/pink-colour-surgery</a> Their other albums lined up for further listening whilst working on new incoming bulk <a href="https://mastodon.social/tags/RNAseq" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#RNAseq</a> data. 👌 <a href="https://mastodon.social/tags/LooseEnds" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#LooseEnds</a> <a href="https://mastodon.social/tags/ThePsychoticMonks" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#ThePsychoticMonks</a> <a href="https://mastodon.social/tags/bandcamp" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bandcamp</a> <a href="https://mastodon.social/tags/PostPunk" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#PostPunk</a>

Bgee databaseBgee has a new look! We have officially switched to the new Bgee website. Check us out at <a href="https://www.bgee.org/" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://www.bgee.org/</a> <a href="https://mstdn.science/@SIB" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@SIB</a> <a href="https://genomic.social/tags/scRNAseq" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#scRNAseq</a> <a href="https://genomic.social/tags/RNAseq" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#RNAseq</a> <a href="https://genomic.social/tags/singlecell" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#singlecell</a> <a href="https://genomic.social/tags/GeneExpression" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#GeneExpression</a> <a href="https://genomic.social/tags/bgee" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bgee</a> <a href="https://genomic.social/tags/biocuration" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#biocuration</a> <a href="https://genomic.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bioinformatics</a>

Bgee databaseWe are proud to announce the release of Bgee 15.2 with the addition of thousands of single-cell 10X Genomics and bulk RNA-Seq libraries to allow for more meaningful gene expression comparisons across species. We also added the free text anatomical, developmental and cell type information provided by authors in addition to the standardized ontology terms. <a href="https://www.bgee.org/" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://www.bgee.org/</a> <a href="https://genomic.social/tags/scRNAseq" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#scRNAseq</a> <a href="https://genomic.social/tags/RNAseq" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#RNAseq</a> <a href="https://mstdn.science/@SIB" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@SIB</a>

Daniel E. WeeksSTATGEN 2024 talk Statistical Methods for Single-Cell RNA-Seq Analysis and Spatial Transcriptomics Rafael IrizarrytSNE and UMAP plots: "They really aren't informative, but they are really pretty."Negative control scRNAseq data set: the percent of zeros is very high, and contributes strongly to the first PCA. tSNE plot 'discovers' new cells.Transformed to log2(1 + CPM): looks zero-inflated.Raw counts: Poisson1/<a href="https://fediscience.org/tags/Genetics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Genetics</a> <a href="https://fediscience.org/tags/STATGEN2024" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#STATGEN2024</a> <a href="https://fediscience.org/tags/StatisticalGenetics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#StatisticalGenetics</a> <a href="https://fediscience.org/tags/RNAseq" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#RNAseq</a> <a href="https://fediscience.org/tags/Transcriptomics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Transcriptomics</a>

Dr. Robert M FlightWhat RNA-Seq datasets are everyone using for RNA-Seq differential analysis workshops, using {DESeq2} or {limma} <a href="https://mastodon.social/tags/RStats" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#RStats</a>? Two or three categories, and ideally a good (4 or 5+) number of replicates, human or mouse?We have some new methods in ontology enrichment, and we really could use some more datasets to try them on.I've found the {airways} dataset, and lung adenocarcinoma from {recount3} (as an easy pull). Looking for others. TIA. <a href="https://mastodon.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bioinformatics</a> <a href="https://mastodon.social/tags/RnaSeq" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#RnaSeq</a>

Frank AylwardWho are giant viruses infecting in the ocean?In a collaborative paper with the Vardi lab, we were able to link many giant virus lineages to protist hosts using <a href="https://genomic.social/tags/SingleCell" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#SingleCell</a> <a href="https://genomic.social/tags/RNASeq" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#RNASeq</a>. One <a href="https://genomic.social/tags/protist" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#protist</a> host (leucocryptos) made up less than 1% of the community, but we could still identify a cryptic viral lineage infecting it, leading to population collapse. <a href="https://www.nature.com/articles/s41564-024-01669-y" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://www.nature.com/articles/s41564-024-01669-y</a><a href="https://genomic.social/tags/marine" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#marine</a> <a href="https://genomic.social/tags/viruses" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#viruses</a> <a href="https://genomic.social/tags/microbiology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#microbiology</a>

Bgee databaseWe are excited to announce a new training course on Bgee 🧬 Course: Gene Expression made Useful Easily: Tools and Database of Bgee Date: Friday 31 May 2024 Taught by: the Bgee team (Frédéric Bastian and Marc Robinson-Rechavi) Apply at: <a href="https://sib.swiss/training/course/20240531_BGEEL" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://sib.swiss/training/course/20240531_BGEEL</a> <a href="https://genomic.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bioinformatics</a> <a href="https://genomic.social/tags/training" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#training</a> <a href="https://genomic.social/tags/RNAseq" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#RNAseq</a> <a href="https://genomic.social/tags/singlecell" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#singlecell</a> <a href="https://genomic.social/tags/GeneExpression" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#GeneExpression</a> <a href="https://genomic.social/tags/bgee" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bgee</a>

Frank AylwardIf you are annotating genes in a eukaryotic genome with <a href="https://genomic.social/tags/rnaseq" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#rnaseq</a> , how do you handle antisense transcripts? It seems like they are quite common in many situations. I'm using tophat + stringtie, and sometimes I see features being called on the wrong strand. <a href="https://genomic.social/tags/transcriptome" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#transcriptome</a> <a href="https://genomic.social/tags/transcriptomeAnalysis" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#transcriptomeAnalysis</a> <a href="https://genomic.social/tags/RNA" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#RNA</a> <a href="https://genomic.social/tags/mRNA" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#mRNA</a>

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