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Pegasus
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resug
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Recent Replies
Comment: Help with running ATAC using Encode pipeline
by
rfran010
▴
160
> I am not sure what to put in the input file. Is it something like
> this?
What input file are you referring to? Your fastqs are given in…
Comment: retaining only the clusters of interest
by
rfran010
▴
160
I usually use select to choose which columns to keep, but not sure if this subset function is specific to seurat ( I am completely unfamili…
Comment: Limma returned only positive logFC values
by
melissachua90
▴
40
I added the dput. Thanks for the reminder!
Comment: Limma returned only positive logFC values
by
Gordon Smyth
★
6.1k
Please show the design matrix or the code used to create the design matrix.
The result you report is a common occurrence when people mista…
Comment: What does "OS_CNSR" and "PFS_CNSR" mean?
by
GenoMax
129k
[**From this doc**][1]: **CNSR** variable is created based on the event occurrence and the values are 0 (when the event
occurs) and 1 (comp…
Answer: How to run Picard docker image
by
geocarvalho
▴
330
I had the same issue, but I found out in the previous GitHub issues that it was made in a way to run like this:
```bash
docker run broadins…
Comment: calculate p value and associated z score for snp-gene pair
by
rheab1230
▴
140
Thank you so much for the information.
Comment: Gviz Coverage Plots
by
Ram
39k
I understand that but stick to one place at least for a while and always link to other places you've posted (reasonable places, we don't ne…
Comment: Gviz Coverage Plots
by
Researcher
•
0
Sorry, I didn't know that posting it on another forum was rude but I really need help with this.
Comment: Correct way to remove Nextera adapters from ITS sequences
by
mattze731
▴
10
Trimmomatic allows to enter custom adapter sequences, but I don't see how this would change the outcome. Similarly, trimmomatic also allows…
Comment: phage genome submission in ncbi genebank
by
acvill
▴
290
When running prokka, did you call the `--compliant` parameter to enforce Genbank compliance? https://github.com/tseemann/prokka#ncbi-genban…
Comment: Correct way to remove Nextera adapters from ITS sequences
by
Trivas
★
1.2k
Some of these programs have a minimum size threshold for a read to be retained. You could play around with that to keep all trimmed reads 5…
Comment: retaining only the clusters of interest
by
seidel
11k
Could it be that idents needs a character string instead of integers? Also, you have an extra comma in your call after c(0:16).
Comment: retaining only the clusters of interest
by
Ram
39k
`idents` is probably a factor so even though you've removed cells with those level values, the factor level still remains. Don't worry abou…
Comment: Contigs to chromosomes annotation
by
GenoMax
129k
I would still recommend using `minimap2` and aligning against reference. It should go pretty fast. You can either work with PAF (default) f…
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