User: darbinator

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darbinator220
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Posts by darbinator

<prev • 49 results • page 1 of 5 • next >
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Answer: A: How to map a set of genes on a circular representation of DNA ?
... 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 darbinator220
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Perform two-way ANOSIM in R
... 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 ...
metabarcoding R metagenomic statistics written 9 weeks ago by darbinator220 • 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 darbinator220
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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 darbinator220
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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 darbinator220
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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 darbinator220
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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 darbinator220 • updated 8 months ago by RamRS25k
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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 darbinator220
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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 darbinator220
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Answer: A: STAR mapping pipeline with 2-pass for multiple samples?
... 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 darbinator220

Latest awards to darbinator

Popular Question 5 months ago, created a question with more than 1,000 views. For How to do gene functional annotation ?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Arabidopsis thaliana transcriptome annotation
Scholar 9 months ago, created an answer that has been accepted. For A: Arabidopsis thaliana transcriptome annotation
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Arabidopsis thaliana transcriptome annotation

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