User: jordi.planells

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Posts by jordi.planells

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Comment: C: How to find differential expression in lowly expressed transcripts?
... Sorry to bother with this simple question, but does this apply as well for p_value and p_adjusted of DESeq2 output?? Thanks! ...
written 8 weeks ago by jordi.planells230
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Answer: A: checking overlap between two genomic coordinates
... You can also try `bedtools intersect`. See [here][1] for more details [1]: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html ...
written 9 weeks ago by jordi.planells230
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Comment: C: SRA tool kit
... If you install it with conda you won't have to configure anything ...
written 3 months ago by jordi.planells230
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Comment: C: How to handle 4 fastq file for one paired-end sample?
... In public data there are only 2 files (R1 and R2) because the concatenation (the cat command) of the different lanes has already been performed. Recap: To merge the different lanes, use `cat` To merge different bam files (for example several replicates) use `samtools merge` ...
written 3 months ago by jordi.planells230
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Answer: A: How to handle 4 fastq file for one paired-end sample?
... Hi! I think what you have there is 2 fastq files for the same sample, each one coming from a different sequencing lane (note that some of the files have L001 and some others L002). What you need to do is to concatenate the sequencing lanes into one file and then align with the resulting file. ...
written 3 months ago by jordi.planells230
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Comment: C: Why Salmon produces different quantification results compared with featureCounts
... Have you realigned allowing multimappers? If you run featureCounts on the same bam file (in which you have filtered out the multimappers) won't do any difference. I have been using featureCounts with and without the -M flag and definitely I see a difference in the quantification. I can suggest you t ...
written 3 months ago by jordi.planells230
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Answer: A: Why Salmon produces very different quantification results compared with featureC
... As far as I know, salmon takes multimappers into account, maybe there you find the difference. Could you align with STAR allowing multimappers, quantify with featureCounts with -M flag and get the correlation again? I am very curious on how this will behave ...
written 3 months ago by jordi.planells230
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Answer: A: One sample Wilcoxon test for each boxplot ggplot2
... In case anyone faces the same problem, I will paste the code I used to get the plot. # Subset the dataset into different knockdowns A = com_sig.df[com_sig.df$Knockdown=="A",] B = com_sig.df[com_sig.df$Knockdown=="B",] C = com_sig.df[com_sig.df$Knockdown=="C",] # Compute the ...
written 3 months ago by jordi.planells230
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Comment: C: One sample Wilcoxon test for each boxplot ggplot2
... Thank you so much! This work smoothly! I am pasting the code with the answer and closing the question ...
written 3 months ago by jordi.planells230
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Comment: C: One sample Wilcoxon test for each boxplot ggplot2
... One p-value for each biotype (or boxplot) in each facet. In other words, if I have 6 boxplots per facet, I should get 6 p-values per facet ...
written 3 months ago by jordi.planells230

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Scholar 3 months ago, created an answer that has been accepted. For A: One sample Wilcoxon test for each boxplot ggplot2
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: One sample Wilcoxon test for each boxplot ggplot2
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: One sample Wilcoxon test for each boxplot ggplot2
Scholar 3 months ago, created an answer that has been accepted. For A: One sample Wilcoxon test for each boxplot ggplot2
Epic Question 10 months ago, created a question with more than 10,000 views. For geom_bar plot with several variables
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