User: Carlo Yague

gravatar for Carlo Yague
Carlo Yague3.0k
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Belgium
Last seen:
3 days, 13 hours ago
Joined:
1 year, 10 months ago
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c**********@gmail.com

Posts by Carlo Yague

<prev • 423 results • page 1 of 43 • next >
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Comment: C: How to install Arlequin R package?
... What kind of graphs ? ...
written 3 days ago by Carlo Yague3.0k
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Comment: C: Lots of antisense transcripts in my annotation?
... *Natural antisense transcript are very common*, but they are usually not defined as coming from the same gene as the sense transcript. In a "normal" annotation, you should have the main gene composed of only sense transcripts isoforms, and a possible anti-sense gene made of only anti-sense transcrip ...
written 3 days ago by Carlo Yague3.0k
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Answer: A: How to install Arlequin R package?
... There is a [function to create arlequin files][1] in the package strataG. If this is what you are looking for, try install.packages('strataG') Edit : have you tried a [simple search][2] on RDocumentation ? There are a few functions to work with arlequin files. [1]: https://www.rdocumentat ...
written 3 days ago by Carlo Yague3.0k
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Comment: C: samtools sort stuck during merging
... Ok, I just tried that (I had little hope) but **IT WORKED** ! Thank you ! But WTF is going on ? samtools sort used to work perfectly well with stdout... ...
written 11 days ago by Carlo Yague3.0k
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Answer: A: Clustering and Bedtools
... To do what you want with cluster : 1) Input file : bed file of the two TFs binding site with a field refering to the TF. ex : chr1 100 150 TF1 chr1 180 230 TF2 chr1 250 280 TF1 chr1 950 1000 TF2 2) Find clusters within a reasonable window (for instance 500 bp). bedtools cl ...
written 11 days ago by Carlo Yague3.0k
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samtools sort stuck during merging
... Hi ! I got a new computer recently and had to re-install samtools (version 1.5) and a few other programs. Now when I try to sort a bam file, everything goes well (samtools creates all those little intermediate files) until the merging process : [bam_sort_core] merging from 58 files... Then i ...
next-gen samtools bamtools sort written 12 days ago by Carlo Yague3.0k
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Comment: C: Clustering and Bedtools
... > I want my clusters to be made of 2 parts of TF1 and 1 part of the TF2 `cluster` doesn't work with "parts" : your TF binding sites is either included in a cluster, or not. Also, note that the configuration you ask for (2 TF1 and 1 TF2 binding sites included in a cluster) can not be enforced usi ...
written 12 days ago by Carlo Yague3.0k
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Comment: C: How to open bedgraph file in bedGraphtoBigWig
... > I installed and opened it already I will state the obvious just to make sure that there is not a misunderstanding here : programs like bedGraphtoBigWig do not really "open" (like by double-clicking on it). Instead, you need to run the program from a UNIX shell. ...
written 17 days ago by Carlo Yague3.0k
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Comment: C: How to collapseReplicate in DESeq2
... **Should you collapse replicates ?** Probably yes (for technical replicates). **How should be the design ?** Look [here][1] for examples of time course analysis in DESeq2. Hope this helps. If you need a more elaborated answer, create a new question with all the details, as suggested by WouterDeCos ...
written 19 days ago by Carlo Yague3.0k
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Comment: C: how can I see the coverage of my own BED file on UCSC Genome Browser?
... > But the IGV always crashed because of the low memory ... You should probably use indexed binary format, such as [bigbed][1] for annotation files or [bigwig][2] for coverage files. Those file are smaller than wig/bed/bedgraph files and don't need to be fully loaded in the genome browser, meani ...
written 19 days ago by Carlo Yague3.0k

Latest awards to Carlo Yague

Teacher 11 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 11 days ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 19 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 19 days ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Scholar 8 weeks 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 4 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
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 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 4 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Scholar 4 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
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
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: The bed12 format
Scholar 4 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
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
Popular Question 4 months ago, created a question with more than 1,000 views. For Intron-aware coverage for paired-end RNA-seq 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
Scholar 5 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
Commentator 6 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 6 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene

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