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Comment: Low Alignment rate
by
dsull
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4.7k
Wow! Didn't realize the repeat-masked file could have such a large influence on alignment. Very good to know -- I guess I'll need to dive i…
Comment: Troubles launch IGV on Linux(Debian)
by
morovatunc
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550
Disclaimer: My comment could be totally unrelated. I would give these a try if you have noone comment/answer your problem.
I have had this…
Comment: How to check RNAseq support for annotated genes?
by
Michael
53k
> I tried it using STAR to map the transcript to the annotation gtf file
That is not what STAR is for. STAR is for aligning short reads in…
Comment: Low Alignment rate
by
Mehwish
•
0
Thanks alot! This worked out for me https://ftp.ensembl.org/pub/release-110/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz …
Comment: Violin plot (Monocle 3) - Troubleshooting
by
Ram
40k
The error message tells me there is the possibility of a conflicting function called `plot_genes_violin` that accepts one parameter and err…
Comment: Violin plot (Monocle 3) - Troubleshooting
by
bk11
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I m not sure why you have problem there. I do not encounter any problem. May be your gene list are not present in your source object. Pleas…
Comment: Violin plot (Monocle 3) - Troubleshooting
by
Ram
40k
What is the output to:
```r
help.search('plot_genes_violin', agrep=FALSE, ignore.case=FALSE, fields=c('name'))
lsf.str()
sessionInfo()
```
Comment: Violin plot (Monocle 3) - Troubleshooting
by
seattlescientist_01
•
0
I see the error message but I'm confused on what it's telling me.
Answer: Bacterial Pangenome Analysis
by
liorglic
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1.2k
I am not sure I understand why you think there is a problem with your analysis. It makes perfect sense that different blastp cutoffs produc…
Comment: How to plot proportion of cells in each cluster with scanpy?
by
bioinfo
▴
110
Thank you for replying again. The "type" still causes issues but the reply by Radu Tanasa worked.
Comment: How to plot proportion of cells in each cluster with scanpy?
by
bioinfo
▴
110
Thank you so much. That worked perfectly and it was much faster than what I was trying.
Answer: How to plot proportion of cells in each cluster with scanpy?
by
Radu Tanasa
▴
60
Hi. If I get this right, you simply need to compute the percentage of cells in each cluster at the dataset level?
```py
import pandas as p…
Comment: Should I Learn Docker to Run Command Line Bioinformatics Tool?
by
ATpoint
76k
Why would that be an advantage?
Comment: How to plot proportion of cells in each cluster with scanpy?
by
bk11
★
1.2k
The following code will write percentage in your stacked barplot.
cross_tab = pd.crosstab(adata.obs['leiden_0.6'],adata.obs['typ…
Comment: How to check RNAseq support for annotated genes?
by
BioinfoBee
•
0
@juke34 Thanks for the suggestion. I wonder if bedtool coverage or intersect can be used to check the transcript support or coverage for ea…
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