- by /u/Mission-Chain-1011I’m aligning PacBio long reads to a draft assembly and want a Circos plot showing contig–contig links supported by single reads (assembly QC, not scaffolding). Should links be built from primary only, primary + supplementary, or include secondary alignments? Any recommended tools or workflows for this visualization are welcome. submitted by /u/Mission-Chain-1011 [link] [comments]
- by /u/EntertainmentOk3181Hello, hope everyone is doing well! I have an upcoming thesis, I have to compare the population structure of genomes using both autosomal (aDNA) and mitochondrial (mtDNA) of chickens. I was provided data in the BAM format and need to compare it with a reference genome, preferably NCBI. I have started by playing around with SAMtools, bcftools, vcf and PLink, but I am lost. Anyone have any advice or potential links that can help?? Would be much appreciated. submitted by /u/EntertainmentOk3181 [link] [comments]
- by /u/According_Arm_9772submitted by /u/According_Arm_9772 [link] [comments]
- by /u/Holodoxasubmitted by /u/Holodoxa [link] [comments]
- by /u/Holodoxasubmitted by /u/Holodoxa [link] [comments]
- by /u/HelpingForDoughnutsGot tired of hearing researchers complain about cluster queues and infrastructure headaches. So I built something. Submit your Nextflow or Snakemake pipeline, pick how many cores you need, get results back. No AWS console, no Terraform, no fighting IT for cluster access. Handles spot preemption automatically so your job doesn’t die mid-run. Works with whatever containerized workflow you’re already using. Scale up for a big alignment or variant calling job, scale back to zero after. You never touch the infrastructure. Still early—looking for people running real pipelines to break it and tell me what’s missing. Free compute credits for honest […]
- by /u/Informal_Wealth_9186For GO / pathway enrichment on genes from filtered VCFs (only callable, high-confidence variants), is it best practice to use a custom background gene set rather than the whole genome? Using clusterProfiler with the universe parameter. Would appreciate confirmation or references. Thanks! submitted by /u/Informal_Wealth_9186 [link] [comments]
- by /u/RunSerious5843submitted by /u/RunSerious5843 [link] [comments]
- by /u/Dear-Elevator9430submitted by /u/Dear-Elevator9430 [link] [comments]
- by /u/Stock-Zebra-8690I am a medical laboratory scientist with one year working experience in a Molecular Pathology lab. All of our tests use real-time PCR. Moving forward, I want to work in a diagnostic genetics lab, or do a Master that involves Bioinformatics and genomics. A lot of diagnostic genetics jobs require experience in NGS and variant curation. So I want to add skills like NGS, variant curation and bioinformatics into my skill sets. Also I will likely be learning about Nanopore sequencing of microbial genomes in my current lab soon. I wonder what online courses should I take or resources should […]
- by /u/Embarrassed-Dog8452submitted by /u/Embarrassed-Dog8452 [link] [comments]
- by /u/mindfulywanderingsubmitted by /u/mindfulywandering [link] [comments]
Mass spectrometry websites, social media, journal feeds, and other links and items of interest to the mass spectrometry community.
