User: Carlo Yague

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Carlo Yague5.0k
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Posts by Carlo Yague

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Answer: A: long-non coding RNA and protein-coding genes correlation
... Hi Seta, If I understand correctly, you have RNA-seq data in at least two conditions and you want to see if the change of expression in the protein coding genes is correlated (positively or negatively) with the change of expression of neighboring ncRNA. I have recently done something similar in y ...
written 12 weeks ago by Carlo Yague5.0k
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Comment: C: Transitioning from Wet Lab to Computational Biology as a PhD Student/Surgeon
... > Definitely, the most important thing is that you will learn more by > doing. --> +1 to this. And since you already have your own RNA-seq dataset to analyse, you are good to go ! ...
written 3 months ago by Carlo Yague5.0k
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Comment: C: Unable to perform merging through cuffmerge
... I see three possibilities: the file does not exist, the file exists but the path is wrong, or you do not have the permissions to access the file (although I think the error message would have been different in that last case). To make sure that the path is correct, try to navigate step by step from ...
written 3 months ago by Carlo Yague5.0k
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Comment: C: Unable to perform merging through cuffmerge
... Then try the command `head /mnt/c/Data/Week4/gencommand_proj4/Day8/transcripts.gtf` in terminal. Does it work ? ...
written 3 months ago by Carlo Yague5.0k
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Comment: C: Unable to perform merging through cuffmerge
... This should be a "question", not a tutorial, but to give you a quick answer, it looks like your `/mnt/c/Data/Week4/gencommand_proj4/Day8/transcripts.gtf` is missing or that the path is incorrect. ...
written 3 months ago by Carlo Yague5.0k
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Comment: C: Differential gene expression analysis by DESeq2
... Good question ! According to [DESeq2 original paper][1], it makes more sense to use method A: > "A common procedure is to disregard genes whose estimated LFC β ir is > below some threshold, |β ir |≤θ *[this is method B here]*. However, this > approach loses the benefit of an easily interp ...
written 4 months ago by Carlo Yague5.0k
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Comment: C: How to get multi mappers from bowtie 1
... If bowtie1 didn't assign mapping quality, then the easiest/best way might be to remap the reads using a more *modern* aligner, then filter as suggested above. If for some reason you do not want to do that, another solution would be to extract alignments whose read name occur more than once in the .b ...
written 4 months ago by Carlo Yague5.0k
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Comment: C: bam file: get date that alignment was run
... I'm not aware of date information directly stored in the bam file, but your operating system should record the date of the last change you did to the file. This can be equivalent to the .bam creation date if the file has not been modified afterwards. To view this, use `CTR + i` or `CMD + i` on the b ...
written 4 months ago by Carlo Yague5.0k
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Answer: C: How to blastn a very short query sequence? Identifying telomeres in assembly
... If you are looking for exact repeats of at least n TTAGGG, you could just perhaps just use grep. ...
written 5 months ago by Carlo Yague5.0k
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Comment: C: How to blastn a very short query sequence? Identifying telomeres in assembly
... The minimal seed length is 7 for blast actually. Still too much for this, unless you blast on two or more tandem repeats. For instance: >query sequence TTAGGGTTAGGGTTAGGG ...
written 5 months ago by Carlo Yague5.0k

Latest awards to Carlo Yague

Teacher 4 months ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: What is the purpose of running Cufflinks without a reference annotation?
Appreciated 8 months ago, created a post with more than 5 votes. For A: DESeq2 proper design setting
Scholar 8 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Scholar 8 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Appreciated 9 months ago, created a post with more than 5 votes. For A: DESeq2 proper design setting
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
Popular Question 9 months ago, created a question with more than 1,000 views. For Splicing-defect analysis with RNA-seq paired-end data
Commentator 12 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 14 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Popular Question 15 months ago, created a question with more than 1,000 views. For Splicing-defect analysis with RNA-seq paired-end data
Popular Question 17 months ago, created a question with more than 1,000 views. For Splicing-defect analysis with RNA-seq paired-end data
Teacher 18 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 19 months ago, created an answer that was upvoted at least 5 times. For A: DESeq2 input for DE analysis
Commentator 22 months ago, created a comment with at least 3 up-votes. For C: What is the purpose of running Cufflinks without a reference annotation?
Teacher 23 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 23 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 23 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 23 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Scholar 2.0 years ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Splicing-defect analysis with RNA-seq paired-end data
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Splicing-defect analysis with RNA-seq paired-end data

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