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  • GitHub - epi2me-labs wf-single-cell
    This workflow extracts cell barcodes and UMIs from 10x-generated single cell libraries It was initially created as a Nextflow port of Sockeye The BLAZE preprint provided useful benchmarking of the original sockeye implementation This assisted in the selection of appropriate thresholds for cell
  • Releases · epi2me-labs wf-single-cell - GitHub
    The wf-single-cell workflow now also correctly handles compressed annotation files as inputs for the Visium HD subworkflow, and fixes an edge case in reporting when cell counts are very low
  • Process `pipeline:snv:split_bam_by_bc (1)` terminated with an . . . - GitHub
    Operating System Ubuntu 22 04 Other Linux No response Workflow Version wf-single-cell v3 3 2-g41a5882 (nextflow version 25 10 0, build 10289) Workflow Execution Command line (Cluster) Other workflo
  • Issue · epi2me-labs wf-single-cell - GitHub
    I can probably hack something together by 1) running both samples independently through the wf-single-cell pipeline with default settings, 2) running gffcompare to generate a joint GTF and then 3) re-running the ONT wf-single-cell pipeline specifying stringtie_opts="-G joint gtf", but I'd like to know if there is a simpler approach
  • wf-single-cell README. md at master - GitHub
    wf-single-cell contains an experimental single nucleotide variant (SNV) calling workflow based on longshot Currently the workflow has been tested with a maximum of 1500 cells, and can be expected to take up 24 hours with a 64 core machine
  • GitHub - maoyongbioinfo wf-singlecell-seekone
    Contribute to maoyongbioinfo wf-singlecell-seekone development by creating an account on GitHub
  • EPI2ME · GitHub
    EPI2ME is a collection of bioinformatics tools, workflows, and resources designed to help researchers analyze nanopore sequencing data Our projects focus on making cutting-edge analysis accessible and reproducible for the scientific community
  • CTAT-LR-FUSION error · Issue #166 · epi2me-labs wf-single-cell - GitHub
    epi2me-labs wf-single-cell Public Notifications You must be signed in to change notification settings Fork 46 Star 95
  • Cannot download workflow for offline usage #179 - GitHub
    Operating System macOS Other Linux No response Workflow Version v3 3 3 Workflow Execution Command line (Local) Other workflow execution No response EPI2ME Version No response CLI command run nf-cor
  • Stringtie stuck assign_features_with_stringtie #187 - GitHub
    Hello, I'm encountering the same issue as in this post referenced below; stringtie is stuck for days on one specific chromosome stringtie -L -c 2 -p 8 -G chr gtf -l chr17 stringtie -o stringtie gf





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