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Recent Replies
Comment: Integrated Seurat object change name of the two conditions
by
Amitm
★
2.2k
Yes, its similar structure. This snippet should add a new metadata column "sample.New" with what you want to do
# Assuming a seurat obj. c…
Comment: Low Alignment rate
by
biofalconch
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960
Yeap, you can sample your reads with `seqtk` like this:
seqtk sample -s100 read2.fq 100 > Sample.fq
Take a couple and run them throug…
Answer: obtaining circular RNAs' sequences from circBase
by
Barry Digby
★
1.2k
You won't find them on circBase.
circAtlas has the mature spliced sequence available. You can [search for circRNAs](https://ngdc.cncb.a…
Comment: Should I Learn Docker to Run Command Line Bioinformatics Tool?
by
Ram
40k
\#TIL mambaforge - better than continuum's conda images I'm guessing?
Comment: Should I Learn Docker to Run Command Line Bioinformatics Tool?
by
arriyaz.nstu
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30
If the laptop doesn't support WSL2, then will the Docker (with linux) work?
Comment: Integrated Seurat object change name of the two conditions
by
camillab.
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130
thanks but my metadata looks different from yours. Will it work even there are not the same "structure"?
or…
Answer: Should I Learn Docker to Run Command Line Bioinformatics Tool?
by
ATpoint
76k
Docker is great, I use it daily since you're independent of the host computer and can share and pull the images via DockerHub. It's also gr…
Comment: Enrichment of mitochondrial and ribosomal pathways - an artifact?
by
ATpoint
76k
If you do DE analysis on single-cell level then I find it critical to enforce some cutoff, as many cells means a lot of power so you get ev…
Comment: Visualize where kmers are on a reference genome
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Ram
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Did you google "visualize BED file on genome"?<a href="" title="Text added because biostars parser needs it"></a>
Comment: obtaining circular RNAs' sequences from circBase
by
Ram
40k
> as you know
No I did not. I know this is a cultural mannerism but it's antiquated. Please abandon this phrase, it can come across as con…
Comment: Enrichment of mitochondrial and ribosomal pathways - an artifact?
by
omer.shomrat
•
0
Thanks a lot for the response!
I'm doing pathway enrichment analysis (using clusterProfiler) on almost all genes in each cluster, with the…
Comment: Unable to build applet in DNAnexus, .jar file not found
by
Ram
40k
Ah I missed the part where DNANexus makes this problem out of our reach. Thank you, GenoMax!
Answer: Unable to build applet in DNAnexus, .jar file not found
by
Ram
40k
That's not how `$PATH` works. Place your jar file in any accessible location, then add a script to your `/usr/local/bin` like so:
```
#…
Comment: Unable to build applet in DNAnexus, .jar file not found
by
GenoMax
134k
Please contact DNANexus support. That may be your best bet since this is commercial software and not many here will have access.
Comment: How to determine the total count for each gene in lymphotype B
by
fracarb8
★
1.2k
A quick way is
# select only B cells
Idents(rds_obj) <- "clusters"
rds_obj <- subset(rds_obj, idents = "lymphocyte B", invert…
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