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Comment: TCGA Germline allelic fraction distribution
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ramiro.barrantes
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Hello, thank you very much for your response. The error was actually in how I am calling Strelka, I ran haplotypecaller on the same data an…
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If you are able to get `unicycler` to run by limiting max k-mer length then that would be the best option since you won't lose the addition…
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Can you post examples of a few reads that have survived the pre-processing you did.
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I don't think this has anything to do with `STAR` and its splice-aware nature. This sequence is not present in your data as we proved with …
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Thank you for the insightful feedback. You’re absolutely right, and I’d like to clarify the duplication rates:
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most (all?) mitochondrial genomes are circular so you can actually 'cut' them to a linear representation anywhere you want.
(by which I m…
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This might be a mapping quality issue since many identical sequences are in mirBase.
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- align vs the genome they were gener…
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I managed to detect my gene, I think the problem was related to the gtf missing some fields, but with
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You can try to take a look this: [link_papaer][1]
[1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC11529866/
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sorry for the misunderstanding. After setting the number of kmers to be below the length of the shorter reads, `unicycler` runs smoothly (t…
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you mean assemble them into pseudo-chromosomes or identify which scaffold is derived from which 'real' chromosome?
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Looks like this is a 10x single cell dataset. You should download the BAM file linked from https://trace.ncbi.nlm.nih.gov/Traces/?view=run_…
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https://www.biostars.org/p/9612137/ is the question on Biostars, that was also posted to GitHub.
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What do you need to know that is not not captured in the online documentation?
Comment: Normalization Of Rna Sequencing Counts (By Ercc / Gene Length)
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Stephan
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`elementLengths()` was renamed > 8 yrs ago; the current generic is `elementNROWS()` (or simply `lengths()`).
```R
# replace just this line…
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