User: Carlo Yague

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Carlo Yague4.5k
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Posts by Carlo Yague

<prev • 576 results • page 1 of 58 • next >
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Answer: A: DESeq2 converting numeric to factor for unknown reason
... > "some variables in design formula are characters, converting to > factors". But there are no character values in the supplied data > frame, and certainly not in the column 'ovaries'! This is probably the key to your problem, there must be hidden character values in ovaries that you are n ...
written 6 days ago by Carlo Yague4.5k
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Answer: A: Differential gene expression analysis by DESeq2
... There are two confusions here. First, `log2FC 1 = FC 2` is true. However, `lfcThreshold`in the first instance is also in log (thats what the first letter "l" stand for) ! So if you want to compare your two methods, you should use the same value for the log2 threshold (1 for instance). Now that this ...
written 16 days ago by Carlo Yague4.5k
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Answer: A: Batch effect, how to create a model matrix
... > At first glance, by looking at the PCA plot from this experiment, how > can you determine (i.e. be absolutely sure) that your samples are > biased or not: I think it is safe to assume that there is always some technical bias in an experiment. So rather than determining whether your sampl ...
written 25 days ago by Carlo Yague4.5k
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Comment: C: Subsampling one bamfile multiple times?
... > Does view -s actually break read pairs? I had this issue once, but it could have been with an older samtools version. Thx for bringing this up, I may try samtools again then. ...
written 7 weeks ago by Carlo Yague4.5k
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Comment: C: RNA-seq: is there a way to get the variability between biological replicates ?
... Wouter's suggestion is probably the most straightforward (you first normalize, scale in log, then compute the correlation). For the normalization, there are many options available. Quantile normalization is a bit uncommon for RNA-seq data, I would rather suggest using the normalization and [rlog tra ...
written 12 weeks ago by Carlo Yague4.5k
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Answer: C: Subsampling one bamfile multiple times?
... Then you should combine samtools with a for loop in a bash script. For instance to subsample multiple files multiple times at multiple depth, you could use this code (untested). #!/bin/bash # down-sample multiple bam files (given as input) 100 times for K fractions (1, 5, 10, 25 % in t ...
written 12 weeks ago by Carlo Yague4.5k
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Comment: C: Subsampling one bamfile multiple times with 1x, 2x, 5x coverage?
... > I tried to use samtools and sambamba but nothing could make accurate > results. What do you mean by that ? I used samtools for subsampling and it worked pretty well with the `-s` option. Of course you need to determine beforehand what fraction of your bam files corresponds to 1x, 2x, 5x cov ...
written 12 weeks ago by Carlo Yague4.5k
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Comment: C: DESeq2 model design
... Ok, but as I said, in your design, sample uninfected and sample on Day0 are basically the same, that is why u get the error. As long as you include the interaction between "condition" and "time", the error will be there. In my proposed workaround, even if you can't compare uninfected with mock dire ...
written 12 weeks ago by Carlo Yague4.5k
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Answer: A: DESeq2 model design
... Hi, First of all, if think that there are typos in your conditions as sometimes you write (un)infe**tc**ed (instead of infe**ct**ed). Your design is not full rank because all "uninfected" are on "day0". A possible solution (that may or may not be good depending on your experimental settings) could ...
written 12 weeks ago by Carlo Yague4.5k
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Comment: C: Extract reads from bam/sam files using read id
... try to remove the "\" except those at the end of the lines. For instance: java -jar $EBROOTPICARD/picard.jar FilterSamReads I=usritt.bam O=output.bam READ_LIST_FILE=keep.txt FILTER=includeReadList ...
written 3 months ago by Carlo Yague4.5k

Latest awards to Carlo Yague

Scholar 20 days ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Splicing-defect analysis with RNA-seq paired-end data
Popular Question 3 months ago, created a question with more than 1,000 views. For Splicing-defect analysis with RNA-seq paired-end data
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: DESeq2 input for DE analysis
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: What is the purpose of running Cufflinks without a reference annotation?
Scholar 9 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Scholar 9 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Scholar 10 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Popular Question 10 months ago, created a question with more than 1,000 views. For Splicing-defect analysis with RNA-seq paired-end data
Popular Question 10 months ago, created a question with more than 1,000 views. For Splicing-defect analysis with RNA-seq paired-end data
Good Answer 12 months ago, created an answer that was upvoted at least 5 times. For A: The bed12 format
Scholar 13 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Popular Question 14 months ago, created a question with more than 1,000 views. For Splicing-defect analysis with RNA-seq paired-end data
Scholar 14 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Scholar 16 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Scholar 17 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Popular Question 17 months ago, created a question with more than 1,000 views. For Intron-aware coverage for paired-end RNA-seq data.

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