User: VHahaut

gravatar for VHahaut
VHahaut1.1k
Reputation:
1,060
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Location:
Belgium
Twitter:
Vincent_Hahaut
Last seen:
11 hours ago
Joined:
2 years, 11 months ago
Email:
v*************@gmail.com

Posts by VHahaut

<prev • 125 results • page 1 of 13 • next >
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Differential expression: High variability inter-samples
... Hi! We recently had to run a differential expression analysis involving RNA-seq from ~20 tumors against several controls. Our final goal was to extract the main differences between our cases and controls. While running DESeq2 on these samples we observed a relatively high variation between cases (w ...
deseq2 limma edger written 3 days ago by VHahaut1.1k
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Minimap2: supplementary alignment PAF
... Hi! I am trying to parse PAF file generated from minimap2.1 to get primary and supplementary alignments of reads but excluding secundary alignments. In SAM format I would search for flags: 0, 16, 2048 and 2064. Unfortunately I don't currently find a nice way to get the same information out of PAF ...
minimap2 written 24 days ago by VHahaut1.1k
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Comment: C: using biomaRt in R to annotate SNPs to Genes within 1000kb
... As explained in the warning message, it seems that your query (snp.gr) and your subject (annot.gr) have some chromosome names which are not in common. This is a warning not an error so if you expect different chromosome names there is nothing to fix. ...
written 7 weeks ago by VHahaut1.1k
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Comment: C: how to add inline barcode to raw DNA fragment without PCR
... As you mentionned it in your question this type of issue can be solved by using a ligase (i.e. T4 ligase) with or without a preliminary restriction enzyme step. Design can be done by hand since the oligo is relatively simple. Synthesis depends on the length of your fragment, most compagnies selling ...
written 5 months ago by VHahaut1.1k
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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 7 months ago by VHahaut1.1k
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Comment: C: Processing barcoded sequencing data
... What are those barcodes exactly, unique molecular identifiers? ...
written 7 months ago by VHahaut1.1k
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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 7 months ago by VHahaut1.1k
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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 7 months ago by VHahaut1.1k • updated 7 months ago by Charles Plessy2.5k
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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 7 months ago by VHahaut1.1k
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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 8 months ago by VHahaut1.1k

Latest awards to VHahaut

Guru 7 months ago, received more than 100 upvotes.
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Up-to-date Online RNA Sequence Analysis Training/Courses/Papers?
Scholar 8 months ago, created an answer that has been accepted. For A: miRNA corresponds to multiple ensembl gene IDs
Popular Question 8 months ago, created a question with more than 1,000 views. For DESeq2 analysis: huge number of outliers and refitting
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Up-to-date Online RNA Sequence Analysis Training/Courses/Papers?
Scholar 9 months ago, created an answer that has been accepted. For A: miRNA corresponds to multiple ensembl gene IDs
Popular Question 9 months ago, created a question with more than 1,000 views. For DESeq2 analysis: huge number of outliers and refitting
Centurion 9 months ago, created 100 posts.
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Up-to-date Online RNA Sequence Analysis Training/Courses/Papers?
Commentator 13 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 13 months ago, created a post with more than 5 votes. For C: Is going back to the wet lab worth it?
Good Answer 17 months ago, created an answer that was upvoted at least 5 times. For C: Is going back to the wet lab worth it?
Appreciated 17 months ago, created a post with more than 5 votes. For C: Is going back to the wet lab worth it?
Teacher 17 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 21 months ago, created a question with more than 1,000 views. For DESeq2 analysis: huge number of outliers and refitting
Student 21 months ago, asked a question with at least 3 up-votes. For MA plots DESeq: strange MA plots
Supporter 21 months ago, voted at least 25 times.
Teacher 22 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 2.1 years ago, created a question with more than 1,000 views. For DESeq2 analysis: huge number of outliers and refitting
Student 2.9 years ago, asked a question with at least 3 up-votes. For MA plots DESeq: strange MA plots

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