User: Carlo Yague

gravatar for Carlo Yague
Carlo Yague2.7k
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Posts by Carlo Yague

<prev • 379 results • page 1 of 38 • next >
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Comment: C: error with number of fields in bedtools
... Have you checked that there is no "invisible" tabulation at the end of some lines of filea (such as line 5) ? ...
written 8 hours ago by Carlo Yague2.7k
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Answer: A: How to turn a FPKM table in a matrix that can be analyzed in R?
... > I was wondering which tool to use and how? Try the [read.table][1] function in R. > And how to import this matrix output by DEseq or EdgeR? I'm not sure to understand, but if you want to use FPKM data in DEseq or EdgeR, this is a bad idea. Those tools require raw counts as input. [1]: ...
written 7 days ago by Carlo Yague2.7k
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Comment: C: filtering genes out from bam file using samtools
... nice catch, I edited, thank you ! ...
written 10 days ago by Carlo Yague2.7k
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Comment: C: How to exclude noisy CNV from study?
... Just a suggestion : you could try to use [CNV-seq][1] that does more or less the same kind of analysis, but calculate automatically the 'optimal' segment size based on the read coverage. That make sense because higher read coverage gives more power to detect differences over smaller segments. [1 ...
written 11 days ago by Carlo Yague2.7k
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Answer: A: Count non-zero elements along the column and append to table in R
... > This is how I did it for rows: myfile$rowsum <- rowSums(myfile[4:6] !=0) Shouldn't it be `rowSums(myfile[,4:6])` ? > For columns I am trying to make this one work, but it starts from the 1st column and not the 4th: rbind(myfile, colSums(myfile != 0)) Try `rbind(myfile, c("colsum", "NA" ...
written 12 days ago by Carlo Yague2.7k
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Answer: A: SpliceR visualization tool
... Have you looked at the [SpliceR vignette][1] ? They show how to make Venn diagrams to analyse results. > After running spliceR(), annotating the spliceRlist object with > information about alterna- tive splicing events. the spliceRPlot() > function can be used for initial data exploration. ...
written 12 days ago by Carlo Yague2.7k
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Answer: A: RNASeq differential expression: How to deal with few genes with extremely high e
... > But my main concern is the gene expression - you can see in the read > distribution plots that there are a few genes with extremely high > expression levels. This is very typical of RNA-seq experiments. You should take the log if you want to see something in the distribution of the un-no ...
written 12 days ago by Carlo Yague2.7k
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Comment: C: How to exclude noisy CNV from study?
... Thx for clarifying. I'm not very familiar with varscan and DNAcopy, but perhaps using longer segments could help stabilize the log ratio. ...
written 12 days ago by Carlo Yague2.7k
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Comment: C: Trimmomatic -> STAR
... I usually align using only the paired reads. In my datasets, there are very few orphan reads (<< 1%) and its not worth the trouble (in my opinion) to incorporate them. But I would be interested to hear a better argumented answer. ...
written 13 days ago by Carlo Yague2.7k
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Answer: A: Basic Help Needed: Download, Cleanup and Merging of Small RNA Libraries.
... Concerning the download, you should install the [sra toolkit][1] and use the command *fastq-dump* in order to convert the sra files into fastq files. [1]: https://www.ncbi.nlm.nih.gov/books/NBK158900/ ...
written 13 days ago by Carlo Yague2.7k

Latest awards to Carlo Yague

Teacher 12 days ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Scholar 12 days ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 12 days ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Scholar 12 days ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Scholar 14 days ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 18 days ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Scholar 18 days ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 23 days 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 days ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Good Answer 23 days ago, created an answer that was upvoted at least 5 times. For A: The bed12 format
Scholar 27 days ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Popular Question 28 days ago, created a question with more than 1,000 views. For Intron-aware coverage for paired-end RNA-seq data.
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Scholar 4 weeks ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Scholar 7 weeks ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Commentator 9 weeks 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 weeks ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Scholar 3 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 3 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 3 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Commentator 4 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 5 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene

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