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Based on the messy-as-heck workflow sketched out in #356, we want to do a number of partial workflows, with specific stopping and restarting points. The workflow I initially had in mind would require …
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### Description of the bug
Viralrecon has worked perfectly for our SCV2 and some hybrid capture protocols (with the metagenomic side). However, when I ran the pipeline by passing a custom bed file an…
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Hello!
I recently sequenced some expanded CD8+ T-cells using a SMART-seq protocol. Given the full-length sequencing I was able to simultaneously capture the TCR-A and/or TCR-B information of most …
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Refers to https://github.com/mskcc/vaporware/issues/101
--- The best approach would be to call blood normal vs. a curated pooled normal of young patients without any hematological malignancies. We …
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The [exRNA Atlas](https://exrna-atlas.org/) is the data repository of the Extracellular RNA Communication Consortium (ERCC). The repository includes small RNA sequencing and qPCR-derived exRNA profile…
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Using free-text entry for the Sequencing Platform field (instrument_model in the submission.xml file) has generated NCBI processing issues in previous submissions. For example, entering "Illumina HiSe…
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## Check for existing package
I have checked the following places for the requested package and could not find
it:
- [x] Poseidon Minotaur Archive
- [x] The `packages/` directory in this r…
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IRIDA should be able to show the user which pipelines they're able to run based on the data available in the cart.
* Ex: If a user has only paired end sequencing data in the cart, only show pipelines…
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Can't run remove_short_reads_SE step because we are missing filter_short_reads_pairs.sh.
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Dear MuPeXI developers,
I read your paper entitled "MuPeXI: prediction of neo-epitopes from tumor sequencing data" at https://doi.org/10.1007/s00262-017-2001-3. In Tables S1, it says that "The f…