User: VHahaut

gravatar for VHahaut
VHahaut1.1k
Reputation:
1,070
Status:
Trusted
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

<prev • 125 results • page 1 of 13 • next >
1
vote
0
answers
365
views
0
answers
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 12 months ago by VHahaut1.1k
0
votes
1
answer
830
views
1
answer
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 12 months ago by VHahaut1.1k • updated 7 months ago by lolec10
0
votes
2
answers
2.9k
views
2
answers
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 13 months ago by VHahaut1.1k
0
votes
0
answers
556
views
0
answers
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 17 months ago by VHahaut1.1k
1
vote
2
answers
823
views
2
answers
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 19 months ago by VHahaut1.1k
0
votes
1
answer
532
views
1
answers
Comment: C: Processing barcoded sequencing data
... What are those barcodes exactly, unique molecular identifiers? ...
written 19 months ago by VHahaut1.1k
1
vote
1
answer
879
views
1
answers
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 VHahaut1.1k
6
votes
1
answer
879
views
1
answer
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 19 months ago by VHahaut1.1k • updated 19 months ago by Charles Plessy2.7k
1
vote
9
answers
1.6k
views
9
answers
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 20 months ago by VHahaut1.1k
0
votes
1
answer
973
views
1
answers
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 VHahaut1.1k

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, created a question with more than 1,000 views. For Conversion sheep/mammal ID to human for GSEA
Voter 11 months ago, voted more than 100 times.
Guru 19 months ago, received more than 100 upvotes.
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Up-to-date Online RNA Sequence Analysis Training/Courses/Papers?
Scholar 20 months ago, created an answer that has been accepted. For A: miRNA corresponds to multiple ensembl gene IDs
Popular Question 20 months ago, created a question with more than 1,000 views. For DESeq2 analysis: huge number of outliers and refitting
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Up-to-date Online RNA Sequence Analysis Training/Courses/Papers?
Scholar 21 months ago, created an answer that has been accepted. For A: miRNA corresponds to multiple ensembl gene IDs
Popular Question 21 months ago, created a question with more than 1,000 views. For DESeq2 analysis: huge number of outliers and refitting
Centurion 22 months ago, created 100 posts.
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: Up-to-date Online RNA Sequence Analysis Training/Courses/Papers?
Commentator 2.1 years 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 2.1 years ago, created a post with more than 5 votes. For C: Is going back to the wet lab worth it?
Good Answer 2.5 years ago, created an answer that was upvoted at least 5 times. For C: Is going back to the wet lab worth it?
Appreciated 2.5 years ago, created a post with more than 5 votes. For C: Is going back to the wet lab worth it?
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Up-to-date Online RNA Sequence Analysis Training/Courses/Papers?
Popular Question 2.7 years ago, created a question with more than 1,000 views. For DESeq2 analysis: huge number of outliers and refitting
Student 2.7 years ago, asked a question with at least 3 up-votes. For MA plots DESeq: strange MA plots
Supporter 2.8 years ago, voted at least 25 times.
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: Up-to-date Online RNA Sequence Analysis Training/Courses/Papers?
Popular Question 3.1 years ago, created a question with more than 1,000 views. For DESeq2 analysis: huge number of outliers and refitting
Student 3.9 years ago, asked a question with at least 3 up-votes. For MA plots DESeq: strange MA plots

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 930 users visited in the last hour