User: VHahaut

gravatar for VHahaut
VHahaut1.0k
Reputation:
1,040
Status:
Trusted
Location:
Belgium
Twitter:
Vincent_Hahaut
Last seen:
14 hours ago
Joined:
2 years, 5 months ago
Email:
v*************@gmail.com

Posts by VHahaut

<prev • 121 results • page 1 of 13 • next >
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Answer: A: How to name the genome in karyoploteR ?
... Regarding your second question the github of karyoplotR is extremely well done: [https://bernatgel.github.io/karyoploter_tutorial//Tutorial/CustomGenomes/CustomGenomes.html][1] You can find "how to plot a custom genome" using a GRanges object (easely constructed using a GTF/GFF file) [1]: htt ...
written 5 weeks ago by VHahaut1.0k
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Comment: C: Processing barcoded sequencing data
... What are those barcodes exactly, unique molecular identifiers? ...
written 5 weeks ago by VHahaut1.0k
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Comment: C: ERCC count matrix smart-seq2
... Thanks for your comments! According to thermoSc. website ERCC-00012 is one of the lowest: ERCC-00012 C 0.11444092 attomoles/ul ...
written 6 weeks ago by VHahaut1.0k
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ERCC count matrix smart-seq2
... Hi! I received some data produced by single-cell sequencing (smart-seq2). After aligning onto the corresponding genome (+ERCC) I got a matrix of count which look quite sparsed: ID start end strand length count1 count2 count3 ERCC-00004 1 523 + 523 1902 145 2328 ERCC-00009 1 984 + 984 ...
rna-seq written 6 weeks ago by VHahaut1.0k • updated 6 weeks ago by Charles Plessy2.3k
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Answer: A: What's fascinating about Bioinformatics for potential students?
... If you are talking to biologists I would put the amount of data you analyze at once and the number of questions you can answer. Doing a PCR or a Western blot takes hours. And you can only assay a few things at once while with bioinformatics skills you can process millions of information in parallel ...
written 6 weeks ago by VHahaut1.0k
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Comment: C: DESeq2 with subset of genes
... In the parental line, when you map to the entire genome, what is the mapping rate on the subset of 300 genes? Could you maybe clarify a bit how you mapped? **Ex**: Parental ==> Mapped to entire genome ==> 90% uniquely mapping Hybrid ==> Mapped to entire genome ==> not working ...
written 7 weeks ago by VHahaut1.0k
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Comment: C: Viral integration studies using RNA-seq data
... Just a possibility since most insertion sites from their RNA-seq are in intronic or intergenic regions: Not all introns are spliced so they might still find some insertions sites from them (with less probability). The same reasoning should work for intergenic regions that are sometimes translated. ...
written 7 weeks ago by VHahaut1.0k
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Comment: C: How to extend the heatmap data points that extended past end of ideogram in circ
... You might have to give a bit more details about your code, package used, example, ... This is not enough to allow us to help you. ...
written 8 weeks ago by VHahaut1.0k
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Comment: C: range of fold change in RNA seq
... Have they been sequenced at the same time? Are the coverages roughly similar (size factors?) ? ...
written 9 weeks ago by VHahaut1.0k
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Comment: C: Stack several manhattan plots
... Using the facet_wrap you'll split your graph in as many chromosome as you have: library(dplyr) library(ggplot2) tmp <- data_frame( CHR=paste0("chr", sample(1:10, 1000, replace=T)), POS=seq(1,1000), pval1=1/runif(n = 1000, min=0, max=0.2), pval2=1/c(runif( ...
written 9 weeks ago by VHahaut1.0k

Latest awards to VHahaut

Guru 6 weeks ago, received more than 100 upvotes.
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Up-to-date Online RNA Sequence Analysis Training/Courses/Papers?
Scholar 9 weeks ago, created an answer that has been accepted. For A: miRNA corresponds to multiple ensembl gene IDs
Popular Question 10 weeks ago, created a question with more than 1,000 views. For DESeq2 analysis: huge number of outliers and refitting
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Up-to-date Online RNA Sequence Analysis Training/Courses/Papers?
Scholar 11 weeks ago, created an answer that has been accepted. For A: miRNA corresponds to multiple ensembl gene IDs
Popular Question 3 months ago, created a question with more than 1,000 views. For DESeq2 analysis: huge number of outliers and refitting
Centurion 3 months ago, created 100 posts.
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Up-to-date Online RNA Sequence Analysis Training/Courses/Papers?
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: Is it normal to have low expression levels of house keeping genes in plant RNA-s
Appreciated 7 months ago, created a post with more than 5 votes. For C: Is going back to the wet lab worth it?
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For C: Is going back to the wet lab worth it?
Appreciated 11 months ago, created a post with more than 5 votes. For C: Is going back to the wet lab worth it?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Up-to-date Online RNA Sequence Analysis Training/Courses/Papers?
Popular Question 14 months ago, created a question with more than 1,000 views. For DESeq2 analysis: huge number of outliers and refitting
Student 14 months ago, asked a question with at least 3 up-votes. For MA plots DESeq: strange MA plots
Supporter 15 months ago, voted at least 25 times.
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Up-to-date Online RNA Sequence Analysis Training/Courses/Papers?
Popular Question 19 months ago, created a question with more than 1,000 views. For DESeq2 analysis: huge number of outliers and refitting
Student 2.4 years ago, asked a question with at least 3 up-votes. For MA plots DESeq: strange MA plots

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