User: MutationalMeltdown

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Posts by MutationalMeltdown

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Comment: C: Force directed graphs compared to other dimensionality reduction methods for scR
... Thanks, the Scanpy docs describes Force-directed graph drawing as "An alternative to tSNE that often preserves the topology of the data better", which I interpreted as meaning that FDGs are used for dimensionality reduction plus viz, otherwise how is it an alternative to tSNE? Also, why are FDGs use ...
written 5 months ago by MutationalMeltdown60
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Comment: C: 'position-aware' aligning of sequences with letter annotations
... The `PairwiseAligner()` offers some different alignment algorithms and a fast C-implementation, but yes it does not solve your issues. The alignment module will 'ingest' `Seq`/`MutableSeq`/`UnknownSeq` objects (not just str) and I'm not sure it would make sense for them to ingest `SeqRecord`s since ...
written 5 months ago by MutationalMeltdown60
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Comment: C: 'position-aware' aligning of sequences with letter annotations
... I don't think there is yet an elegant way to do this in Biopython. In theory the `MutableSeq` class would be well suited for this task, since it handles sequences that are not single characters, but in practise it's not currently maintained in a way that could be used. You can at least use the newer ...
written 5 months ago by MutationalMeltdown60
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Force directed graphs compared to other dimensionality reduction methods for scRNA-seq
... For scRNA-seq visualisation of the transcriptional profiles of cells, people are usually doing PCA, followed by a non-linear dimensionality reduction technique like t-SNE or UMAP. However, some other methods have been suggested for visualisation including diffusion maps and force directed graphs (F ...
scrna-seq rna-seq single cell machine learning written 5 months ago by MutationalMeltdown60 • updated 5 months ago by Jean-Karim Heriche22k
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Comment: C: Understanding kallisto qc metrics in run_info.json
... I posted to the "kallisto-and-applications" forum ...
written 8 months ago by MutationalMeltdown60
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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 9 months ago by MutationalMeltdown60
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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 11 months ago by MutationalMeltdown60
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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 11 months ago by MutationalMeltdown60
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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 11 months ago by MutationalMeltdown60
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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 12 months ago by MutationalMeltdown60

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