User: darbinator
darbinator • 190
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Posts by darbinator
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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 5 weeks ago by
darbinator • 190
0
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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 5 weeks ago by
darbinator • 190
0
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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 7 weeks ago by
darbinator • 190
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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 weeks ago by
darbinator • 190
0
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1
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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 9 weeks ago by
darbinator • 190
• updated
8 weeks ago by
RamRS ♦ 23k
0
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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 10 weeks ago by
darbinator • 190
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2
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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 10 weeks ago by
darbinator • 190
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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 10 weeks ago by
darbinator • 190
1
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0
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209
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... What are these sequences, and why not extract them with the grep function? ...
written 11 weeks ago by
darbinator • 190
0
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2
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227
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... If you want to just count number of AS events in each sample, you have to run these sample again themselfs. For exemples, b1.txt and b2.txt should both been:
Control_1.bam
the PSI scores will obviously be equal to 0 but by counting the number of rows (and thus events) in each of the 5 result files ...
written 11 weeks ago by
darbinator • 190
Latest awards to darbinator
Teacher
11 weeks ago,
created an answer with at least 3 up-votes.
For A: Arabidopsis thaliana transcriptome annotation
Scholar
12 weeks ago,
created an answer that has been accepted.
For A: Arabidopsis thaliana transcriptome annotation
Teacher
12 weeks ago,
created an answer with at least 3 up-votes.
For A: Arabidopsis thaliana transcriptome annotation
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