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Popular Question to
Anand Rao
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Scholar to
andres.firrincieli
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chaco001
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Recent Replies
Comment: Kallisto bustools for scRNA-seq
by
dsull
★
4.0k
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…
Comment: Aberrant splicing in bulk RNAseq
by
dsull
★
4.0k
First thing: kallisto cannot interface with UMI-tools (kallisto doesn't use read headers and therefore you're stuck with "the kallisto way"…
Comment: Using Copy Number Alterations detected in other studies for the same tumor cell
by
lethalfang
▴
90
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…
Comment: Somatic truth set
by
lethalfang
▴
90
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?
by
jv
★
1.0k
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
by
Jeremy
▴
780
g:Profiler has an Arabidopsis option:
[g:Profiler][1]
[1]: https://biit.cs.ut.ee/gprofiler/gost
Answer: Any tips in landing a bioinformatic job?
by
Carambakaracho
★
3.2k
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…
Comment: Best way to visualize .paf or .sam alignment to a fasta file
by
GenoMax
127k
Why not use IGV with SAM file?
If you want a text based viewer then ASCIIGenome: https://asciigenome.readthedocs.io/en/latest/
Answer: What is the NCBI's definition of an "atypical genome"?
by
MirianT_NCBI
▴
500
Hi,
You can find more information about what constitute an [atypical genome in this FAQ][1]. Here's the list of reasons for a genome to …
Comment: How to get subset of a Seurat object based on metadata?
by
sunyeping
▴
80
> skin$predicted_cell_type
Error in rep.int(x = colnames(x = x), times = length(x = i)) : unimplemented type 'NULL' in 'rep3…
Comment: using CITE-seq data to cluster single cells
by
chi.delta
▴
40
Let's say that based on known FACS data, I already know that three populations exist based on the two antibodies staining: single positive …
Answer: syntax errors when running part3 all-against-all
by
Adrian Altenhoff
★
1.0k
Dear Sofia,
this looks like the all-vs-all file is corrupted. maybe a race condition of to processes that tried to write the same file. …
Answer: Any tips in landing a bioinformatic job?
by
zhousun21
▴
40
Since you are just starting out, I suggest sending your resume to a few recruiters who specialize in science placements. They will intervie…
Comment: How to get subset of a Seurat object based on metadata?
by
jv
★
1.0k
Do you have cells labeled "0:CD8 T Cell" in `skin$predicted_cell_type`?
Comment: using CITE-seq data to cluster single cells
by
ATpoint
70k
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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