User: darbinator
darbinator • 220
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Posts by darbinator
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... Maybe Circos ? http://circos.ca
I have never used it but it seems that we can do a lot of things ...
written 8 weeks ago by
darbinator • 220
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... Hi !
I'm not very good at statistics so I want to ask some questions.
I work with metabarcoding 16S dataset
I have generate OTU table from mothur, and I want to know if the differences between samples are more due to one factor (sample site) or from one another (sample hote species)
I have calcu ...
written 9 weeks ago by
darbinator • 220
• updated
7 days ago by
Biostar ♦♦ 20
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Comment:
C: sed or awk command
... It's weird because I try it and it don't remove the others (.) because I didn't put the 'g' global flag after the last slash ...
written 7 months ago by
darbinator • 220
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Answer:
A: sed or awk command
... If the gene is always on the first column:
sed 's/\.[0-9]\{1,\}//' yourfile.txt
should work ...
written 7 months ago by
darbinator • 220
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Comment:
C: How is the design in DESeq2 work?
... Sorry to up this message but when we apply the design " design = ~Strain + Time ", how exactly deseq2 control the effect of Strain in order to test the Time ? It's not clear for me .. ...
written 8 months ago by
darbinator • 220
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Answer:
A: Problem to run checkm.
... According ti the READme:
> By default, CheckM assumes genomes consist of contigs/scaffolds in
> nucleotide space and that the files to process end with the extension
> fna.
>
> Example Usage
>
> Assume you have putative genomes in the directory /home/donovan/bins
> with fa ...
written 8 months ago by
darbinator • 220
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Comment:
C: Adding p-value to box plot
... How is your datatable ?
I used this some weeks ago:
ggplot(mean_expressed, aes(x = mean_expressed$variable, y = mean_expressed$value)) +
geom_boxplot(outlier.colour='black') + stat_compare_means(aes(group = mean_expressed$variable)
`mean_expressed$variable` is a qualitative variable th ...
written 8 months ago by
darbinator • 220
• updated
8 months ago by
RamRS ♦ 25k
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Answer:
A: normalization with RPKM
... DESeq2's (R package) normalisation method seem's to be better than RPKM/FPKM/TPM method for gene count comparisons between samples (source https://hbctraining.github.io/DGE_workshop/lessons/02_DGE_count_normalization.html)
The package take featurecounts table as input and then you canretrieve norma ...
written 8 months ago by
darbinator • 220
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Comment:
C: Analysis rMATS of RNA Seq data
... For the 2 groups, rMATS calculate the IncLevel which is approximately the number of reads that support the inclusion of an event on the number of reads that support the exclusion of the event.
Finally the IncLevelDifference it just the difference between the two IncLevel , calculated by:
IncLevelD ...
written 8 months ago by
darbinator • 220
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... I refer you to the post that I created on the google group linked to the STAR tool, I had the same question as you about the commands related to the 2 pass-mode and the author of STAR answered me:
https://groups.google.com/forum/#!msg/rna-star/4dhcEGFMiK0/XoMh6rB7CwAJ ...
written 8 months ago by
darbinator • 220
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