User: MutationalMeltdown

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Posts by MutationalMeltdown

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Comment: C: Understanding kallisto qc metrics in run_info.json
... I posted to the "kallisto-and-applications" forum ...
written 10 days ago by MutationalMeltdown30
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Understanding kallisto qc metrics in run_info.json
... I've ran `kallisto bus` on multiple read pairs (R1 and R2) fastq files (scRNA-seq 10x data) and I'm trying to understand the QC metrics in `run_info.json`: "n_targets": 0, "n_bootstraps": 0, "n_processed": 286634021, "n_pseudoaligned": 8387513897523690476, "n ...
scrna-seq alignment kallisto rna-seq written 13 days ago by MutationalMeltdown30
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Comment: C: What does a 'normal' FASTQC report look like for scRNA-seq data?
... Thanks! I think the run metrics are okay, but "Reads Mapped to [the mouse] Genome" is 90% for some samples and 80% for others, which is lower than in the 10x example data you linked to where it's over 95% (e.g. [here][1]), would that concern you? [1]: http://cf.10xgenomics.com/samples/cell-exp/3 ...
written 10 weeks ago by MutationalMeltdown30
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Comment: C: What does a 'normal' FASTQC report look like for scRNA-seq data?
... Thanks for the suggestion! I will do that. Perhaps my question is too broad, but the thing that concerns me the most is that there is 1-2bp with slightly lower quality, although not bad enough to fail the "Per base sequence quality" test. These correspond to red blocks on the "Per tile sequence qua ...
written 10 weeks ago by MutationalMeltdown30
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What does a 'normal' FASTQC report look like for scRNA-seq data?
... I'm interested specifically in 'failures' I got on R2 (R1 being just the barcode + UMI). Note this is 10X sincle cell RNA-sequencing (scRNA-seq) data. Test 'failures': - Per tile sequence quality (quality appears slightly worse at about 54bp (the middle of the read), with a corresponding increase ...
scrna-seq 10x fastq rna-seq fastqc written 10 weeks ago by MutationalMeltdown30
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Comment: C: Who are the Greatest Bioinformaticians Of All Time (GBOAT)
... maybe, but Rust-Bio is like Biopython (Peter Cock already rightly mentioned) and people already mentioned Hadley Wickham, who is far more removed from bioinformatics ...
written 3 months ago by MutationalMeltdown30
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Comment: C: Who are the Greatest Bioinformaticians Of All Time (GBOAT)
... Nice list, also surprised no-one mentioned Johannes Köster for Snakemake, Bioconda, and Rust-Bio ...
written 3 months ago by MutationalMeltdown30
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Answer: A: Evolution of Biostars
... The data is interesting but does it answer the question "Which programming language is most frequently used in Bioinformatics"? Other possible factors: - R might be popular on this forum, other languages on other forums- for example, there are 628 [co-tagged][1] R and bioinformatics questions on S ...
written 7 months ago by MutationalMeltdown30

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