User: VHahaut
VHahaut • 1.1k
- Reputation:
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- Location:
- Belgium
- Twitter:
- Vincent_Hahaut
- Last seen:
- 3 months, 1 week ago
- Joined:
- 3 years, 11 months ago
- Email:
- v*************@gmail.com
Posts by VHahaut
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... 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 ...
written 12 months ago by
VHahaut • 1.1k
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... 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 ...
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... 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 13 months ago by
VHahaut • 1.1k
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... 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 17 months ago by
VHahaut • 1.1k
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... 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 19 months ago by
VHahaut • 1.1k
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... What are those barcodes exactly, unique molecular identifiers? ...
written 19 months ago by
VHahaut • 1.1k
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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 19 months ago by
VHahaut • 1.1k
6
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... 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 ...
written 19 months ago by
VHahaut • 1.1k
• updated
19 months ago by
Charles Plessy • 2.7k
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... 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 20 months ago by
VHahaut • 1.1k
0
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973
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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 20 months ago by
VHahaut • 1.1k
Latest awards to VHahaut
Popular Question
6 months ago,
created a question with more than 1,000 views.
For Conversion sheep/mammal ID to human for GSEA
Popular Question
9 months ago,
created a question with more than 1,000 views.
For Conversion sheep/mammal ID to human for GSEA
Popular Question
10 months ago,
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For Conversion sheep/mammal ID to human for GSEA
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19 months ago,
received more than 100 upvotes.
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20 months ago,
created an answer with at least 3 up-votes.
For A: Up-to-date Online RNA Sequence Analysis Training/Courses/Papers?
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20 months ago,
created an answer that has been accepted.
For A: miRNA corresponds to multiple ensembl gene IDs
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20 months ago,
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For DESeq2 analysis: huge number of outliers and refitting
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21 months ago,
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For A: Up-to-date Online RNA Sequence Analysis Training/Courses/Papers?
Scholar
21 months ago,
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For A: miRNA corresponds to multiple ensembl gene IDs
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For DESeq2 analysis: huge number of outliers and refitting
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For A: Up-to-date Online RNA Sequence Analysis Training/Courses/Papers?
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For C: Is it normal to have low expression levels of house keeping genes in plant RNA-s
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For A: Up-to-date Online RNA Sequence Analysis Training/Courses/Papers?
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2.7 years ago,
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For DESeq2 analysis: huge number of outliers and refitting
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For MA plots DESeq: strange MA plots
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For DESeq2 analysis: huge number of outliers and refitting
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3.9 years ago,
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For MA plots DESeq: strange MA plots
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