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Recent Replies
Answer: How to assign gene names after kallisto when I add GFP?
by
dsull
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4.8k
kallisto relies on a transcriptome index, so simply add the GFP sequence to the transcriptome FASTA file and index it. The name in the outp…
Comment: How to convert data in r?
by
Ram
40k
While `%>%` is indeed exported by magrittr, `dplyr` is the most popular package to use them. dplyr imports magrittr, it does not define the…
Comment: Why should ATAC-seq mapped reads be shifted +4 and -5 for +strand and -strand, r
by
suragnair
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0
So long as one's pipeline is consistent throughout, the shift is +4/-4 regardless of 1-based or 0-based indexing. But you're right that shi…
Comment: Why should ATAC-seq mapped reads be shifted +4 and -5 for +strand and -strand, r
by
suragnair
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Each fragment is two cuts (one on + and - strands), which you capture if you do paired-end sequence. Conversely, each cut gives rise to two…
Comment: How to convert data in r?
by
kalavattam
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190
Ah, thanks for pointing that out.
`%>%` is made available with `magrittr`—are pipes in the `dplyr` namespace too? I wasn't aware of that.
…
Answer: Generating a 3D model from 2D slices of a nucleus
by
LChart
3.4k
This question doesn't fit in nicely with the other set of questions (which tend to focus more on omics). However this sounds an awful lot l…
Answer: GOSt Plot
by
bk11
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1.3k
> How do I change the point size on the plot? I know how to do this in
> ggplot, but can't find a command here to do this, even though the…
Answer: The RNA velocity are opposite in 'dynamical' and 'stochastic' modes.
by
james.hawley
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40
Conflicting directions in RNA velocity analysis is not uncommon.
[Gorin _et al._, 2022](https://journals.plos.org/ploscompbiol/article?id=…
Comment: counting from a single BAM file with multiple samples
by
LChart
3.4k
I think you can use UMI-tools to do this with something like `--extract_method=regex --bc-pattern=(?P<cell_1>8)$ --ignore-umi`. However I d…
Comment: counting from a single BAM file with multiple samples
by
bk11
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1.3k
You can do sth like that has been discussed [here][1].
[1]: https://www.10xgenomics.com/resources/analysis-guides/tutorial-navigating-…
Comment: counting from a single BAM file with multiple samples
by
dr-device
•
0
Yes, its from a plate-based protocol but with literally only 20 cells. Im therefore planning on just using edgeR for my analysis rather tha…
Comment: Help with error running velocyto
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bk11
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Sure thing! If it worked, please accept the answer.
Comment: Help with error running velocyto
by
Chris
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200
The tutorial doesn't mention we need to load `samtools`. Thank you so much! You are awesome. It is running now.
Comment: How to extract the first and last 2 nt from multiple sequences in a FASTA file?
by
Ram
40k
Accept this answer to mark the post as solved, and please don't ask the same question again.
Comment: extract first and last n bp from fasta file from multiple fasta file in R
by
Ram
40k
OP asked [the exact same question 2 years ago][1] and got the seqkit subseq answer from shenwei himself. Really odd behavior.
[1]: https…
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