User: Carlo Yague

gravatar for Carlo Yague
Carlo Yague3.3k
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Posts by Carlo Yague

<prev • 462 results • page 1 of 47 • next >
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Comment: C: Why Warning: reads with missing mate encountered is occured in HTSeq?
... > Do I need to sort BAM with -n and run HTSeq Yes, you have to do that in order to have the aligned mates adjacent to each other. Alternatively, featureCounts can sort the reads automaticaly for you before counting. But it will be slow anyway... sorting bam is always a pain. ...
written 12 hours ago by Carlo Yague3.3k
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Comment: C: Completely confused about terminology and what I'm actually analysing here
... > Differential expression study can be tricky since you don't have > transcript length information I disagree. You don't need transcript length information to perform differential expression analysis with DESeq or edgeR and similar raw-counts based methods. In addition, if you really want to ...
written 13 hours ago by Carlo Yague3.3k
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Comment: C: Boxplot in ggplot2
... Yeah I guess this can make sense for time series analysis or things like that... ...
written 6 days ago by Carlo Yague3.3k
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Comment: C: Boxplot in ggplot2
... Nice, but what is the point of connecting the two medians with a red line ? I don't mean to be rude here but unless I'm missing something, that line is just "polluting" the data. ...
written 6 days ago by Carlo Yague3.3k
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Comment: C: Zero read count with deseq2
... Forget about the object "condition", my bad. can you please try again with: coldata$condition=relevel(condition, "untreated") *(this is because `condition` is not the same as `coldata$condition`)* ...
written 9 days ago by Carlo Yague3.3k
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Answer: A: Zero read count with deseq2
... Could it be that instead of testing the expression of the treated vs untreated, your are testing untreated vs treated? To check for that, try to order the levels properly : condition=as.factor(rep(c("UNTREATED", "TREATED"), each=2)) condition [1] UNTREATED UNTREATED TREATED TREATED ...
written 9 days ago by Carlo Yague3.3k
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Comment: C: differential expression analysis
... > what is adjusted p-value i have no idea? Then you should read about it. Search for "[multiple testing correction][1]" and "[adjusted p-value][2]". > how it can be calculate? You can calculate it from a set of uncorrected p-value, see Piechota answerL [1]: https://www.nature.com/article ...
written 9 days ago by Carlo Yague3.3k
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Answer: A: differential expression analysis
... A possible solution is to use adjusted pvalue instead of raw pvalue to account for multiple testing. To illustrate this, imagine that there are 20 000 genes considered in your experiment. With a 5% pvalue cutoff, you accept to have 1000 false positives in your DEGs, which is bad. Instead, you could ...
written 10 days ago by Carlo Yague3.3k
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Comment: C: Low mapping rate for Tophat2
... I would suggest that you [download the reference in fasta][1] and rebuild the index with the above command. Your reference and indexes seem corrupted. [1]: http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/ ...
written 15 days ago by Carlo Yague3.3k
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Answer: A: Low mapping rate for Tophat2
... Warning: Encountered reference sequence with only gaps Have you checked if your reference genome is correct ? Locate the fasta file in ls /home/fadhil/Bowtie2Index/genome Lets say it's called "genome.fa". Then check if it looks good : head /home/fadhil/Bowtie2Index/genome.fa If it i ...
written 16 days ago by Carlo Yague3.3k

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