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Tutorial:
A short primer to pairwise alignment
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Luke Crichton
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updated 5 days ago by
Ram
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written 7.7 years ago by
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Recent Replies
Comment: Kallisto bustools for scRNA-seq
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dsull
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I have no idea what that is besides a bunch of jumbled sequences. You'll need look up the structure of the reads / library from wherever yo…
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First thing: kallisto cannot interface with UMI-tools (kallisto doesn't use read headers and therefore you're stuck with "the kallisto way"…
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There is some somatic SV study on these HCC1395: https://doi.org/10.1186/s13059-022-02816-6.
There is also a CNA preprint from years ago b…
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Just in case things are hard to find, for the WGS/WES, these are the data (what the file names mean: https://sites.google.com/view/seqc2/ho…
Comment: How to get subset of a Seurat object based on metadata?
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Hmm, not sure why `subset` doesn't match to '0:CD8 T cell' but maybe it's the ":"?
An alternative option is the following:
```
idx <- whi…
Comment: GO enrichment analysis
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g:Profiler has an Arabidopsis option:
[g:Profiler][1]
[1]: https://biit.cs.ut.ee/gprofiler/gost
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The first job is a nightmare and you will need some luck. I understand you're looking for an industry offering. Unfortunately I've worked o…
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Why not use IGV with SAM file?
If you want a text based viewer then ASCIIGenome: https://asciigenome.readthedocs.io/en/latest/
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Hi,
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> skin$predicted_cell_type
Error in rep.int(x = colnames(x = x), times = length(x = i)) : unimplemented type 'NULL' in 'rep3…
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Let's say that based on known FACS data, I already know that three populations exist based on the two antibodies staining: single positive …
Answer: syntax errors when running part3 all-against-all
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Dear Sofia,
this looks like the all-vs-all file is corrupted. maybe a race condition of to processes that tried to write the same file. …
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Since you are just starting out, I suggest sending your resume to a few recruiters who specialize in science placements. They will intervie…
Comment: How to get subset of a Seurat object based on metadata?
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Do you have cells labeled "0:CD8 T Cell" in `skin$predicted_cell_type`?
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Think about it, how would any clustering with only two genes/features be informative? Is this really what you need? If you break it down, f…
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