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Deal with duplicated entries. Issue illustrated in the README plot (loci chr4Hg0380431, chr4Hg0383761, or chr5Hg0547031).
Duplicated _loci_ are _locus_ id that appears more than once in the annotat…
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I'm wondering if it would be appropriate to add functionality of reading files such as [`simple_somatic_mutation.open.BRCA-US.tsv.gz`](https://dcc.icgc.org/releases/release_17/Projects/BRCA-US).
Re…
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I read that your tool was used also to assemble the rDNA locus.
I would like to assemble long reads from a single specific gene locus (human) coming from a sequencing experiment in which we should ha…
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Hi--
In processing nascent sequencing data, I really like using multicov to obtain counts over full genes. Ideally, I would like to build this into our nascent Nextflow pipeline. As such, it would …
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A user suggested gramene to include sweet cherry genome. Investigate if there is a sweet cherry genome that meets Epl-Grmene inclusion criteria. ie, published, genome deposited in INSDC, gene annotati…
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I used NOVOPlasty to assemble the mitochondrial genome of my PE shotgun sequencing reads and it's been working fine. But there one sample that is simply not working. I know the sample is good because …
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Dear,
We succesfully implemented CTAT-splicing in our STAR-fusion pipeline.
**1) we pick up all our relevant fusion genes using STARfusion**
**2) we correctly picked up METx14del,** without fal…
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Hi, thank you for developing this excellent software. While using it, I encountered a few issues and would like to suggest some improvements to help optimize and refine the software's functionality.
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Hi Zhenyu,
I noticed in the script S02.umi.process.one.sh, you used minimap2 for mapping to the reference genome and then used salmon for quantification. Additionally, it seems that for the referen…
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I need help!!
I am using pepper_margin_deepvariant variant calling for my target gene but PEPPER is not recognizing my region of interest where I did targeted sequencing using Nanopore. I think this…