User: Carlo Yague

gravatar for Carlo Yague
Carlo Yague2.9k
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Posts by Carlo Yague

<prev • 406 results • page 1 of 41 • next >
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Answer: A: what is the best method to find a conserve amino acid ? and how can I validate i
... > I want to know if any particular method is preferred? if so, which > method? [Clustal][1] is a good start for sequence alignment. But if the structure of your protein is available, a [structural alignment][2] might be worth looking into. > and how can one validate its results? If you ...
written 7 days ago by Carlo Yague2.9k
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Answer: A: Removed rRNAs, tRNAs, snoRNAs, etc. still have FPKM values
... > have not yet checked the bam file to see if there are reads still > mapping to the filtered transcripts. You should definitely try that first. If there are reads mapped at those filtered locations, then it means that HISAT2 mapped some reads that bowtie2 discarded. This would be the most l ...
written 7 days ago by Carlo Yague2.9k
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Answer: A: Normalize bedtools gene coverage by total number of reads
... Hi, It looks like you want to compare the expression of a few genes between conditions. While it is a good start, I think there are a few issues with your method : 1. bedtools is very useful but more specific tools, such as HTseqCounts or featureCounts, are better to count reads on genes. This in ...
written 8 days ago by Carlo Yague2.9k
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Answer: A: htseq read count zero ?
... Have you checked the bottom of the output table ? The number of reads counted as *ambiguous/not_aligned/... [Htseq][1] is possibly more stringent than trinity and could not count mapped reads for several reasons listed here. This could explain why some contigs have zero counts. __no_feature: ...
written 8 days ago by Carlo Yague2.9k
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Comment: C: Interpreting Differentially Expressed Genes(DEGs) from RNA Seq experiment
... I don't think anyone can answer this question without knowing what are the genes affected by Sox2 KO. Anyway, have you tried looking if specific classes of genes are affected ? Perhaps this could help you interpreting your results. ...
written 9 days ago by Carlo Yague2.9k
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Comment: C: Question: combining RNAseq data from different platforms
... What is your goal ? Differential expression analysis ? Do you have some sample that were sequence with both platforms ? If you do, then it should be possible. ...
written 10 days ago by Carlo Yague2.9k
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Comment: C: Correct the error in the code
... As the error states, `next` is to be used within a loop. Type `?next` in the R console for more information. ...
written 25 days ago by Carlo Yague2.9k
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Answer: A: Finding the error in the code
... I guess the second line should be : if ( sum ( is.na ( new_tum[i,] ) ) < dim(new_tum)[2]){ To debug your code yourself, don't be afraid to test it pieces by pieces. The error message in this one was kind of explicit too : every open parenthesis should get closed and vice-versa. ...
written 26 days ago by Carlo Yague2.9k
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Answer: A: Deseq2 multiple comarison
... Looks good to me. From the dds table, you will just need to extract the contrasts now (VD vs wt and AT vs WT) using the `results()` function documented [here][1]. [1]: https://rdrr.io/bioc/DESeq2/man/results.html ...
written 4 weeks ago by Carlo Yague2.9k
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Comment: C: predict RNA polymerase and promoter sequence interaction by auto dock docking
... Do you have the reference of that paper ? I didn't know about that. ...
written 4 weeks ago by Carlo Yague2.9k

Latest awards to Carlo Yague

Scholar 6 days ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 8 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 10 weeks ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Teacher 10 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 10 weeks ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Scholar 11 weeks ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Scholar 11 weeks ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Teacher 12 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 12 weeks ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Good Answer 12 weeks ago, created an answer that was upvoted at least 5 times. For A: The bed12 format
Scholar 3 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Popular Question 3 months ago, created a question with more than 1,000 views. For Intron-aware coverage for paired-end RNA-seq data.
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
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
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?
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
Scholar 4 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Scholar 5 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
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
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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