User: VHahaut

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VHahaut1.1k
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Belgium
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Vincent_Hahaut
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Posts by VHahaut

<prev • 129 results • page 1 of 13 • next >
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scRNA compare gene set enrichment between clusters
... Hello! I am currently exploring a 10x scRNA dataset. I have defined several short gene sets (+/- 10 genes each) that I see expressed at different levels in specific clusters. For each gene set, I would like to summarise the signature at the cluster level and then compare how much one cluster expres ...
scrna written 17 days ago by VHahaut1.1k
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Potential Bacteria Contamination - RNA-Seq
... Hi! I have received a series of human poly-A RNA-seq samples (single-end 75 bp) which display suspicious mapping values. These samples have been mapped with STAR and show +/- 30-50% of reads "unmapped: reads too short". Previous samples done with the same method had only between 5 and 10%. Despit ...
metagenomics rna-seq written 11 weeks ago by VHahaut1.1k • updated 11 weeks ago by genomax91k
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Power Analysis 10x - Minimum number cells per cluster
... Hi! I am analysing a 10x dataset of primary immune cells and found several promising clusters. I would like to compare the gene expression of these clusters however some contain only ~100 cells. I would like to know what are the general recommendations of the community regarding differential expr ...
10x scrna written 11 months ago by VHahaut1.1k
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Nanopore incomplete fragment sequencing
... Hi! I am analysing PCR products sequenced on a MinION from Oxford Nanopore. I observed that some of these reads do not contain both PCR primers, even though the read has been mapped from end to the other. It is like if the PCR product has been sequenced only partially (i.e., from one end to the mid ...
nanopore written 12 months ago by VHahaut1.1k • updated 10 months ago by Biostar ♦♦ 20
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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 2.4 years 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 2.4 years ago by VHahaut1.1k • updated 23 months ago by lolec20
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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 2.5 years 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 2.8 years 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 3.0 years ago by VHahaut1.1k
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Comment: C: Processing barcoded sequencing data
... What are those barcodes exactly, unique molecular identifiers? ...
written 3.0 years ago by VHahaut1.1k

Latest awards to VHahaut

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 9 months ago, created a question with more than 1,000 views. For MA plots DESeq: strange MA plots
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 Conversion sheep/mammal ID to human for GSEA
Popular Question 12 months ago, created a question with more than 1,000 views. For Conversion sheep/mammal ID to human for GSEA
Popular Question 19 months ago, created a question with more than 1,000 views. For Conversion sheep/mammal ID to human for GSEA
Popular Question 19 months ago, created a question with more than 1,000 views. For DESeq2 analysis: huge number of outliers and refitting
Popular Question 22 months ago, created a question with more than 1,000 views. For Conversion sheep/mammal ID to human for GSEA
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Conversion sheep/mammal ID to human for GSEA
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Conversion sheep/mammal ID to human for GSEA
Voter 2.3 years ago, voted more than 100 times.
Guru 3.0 years ago, received more than 100 upvotes.
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: Up-to-date Online RNA Sequence Analysis Training/Courses/Papers?
Scholar 3.1 years ago, created an answer that has been accepted. For A: miRNA corresponds to multiple ensembl gene IDs
Popular Question 3.1 years ago, created a question with more than 1,000 views. For DESeq2 analysis: huge number of outliers and refitting
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: Up-to-date Online RNA Sequence Analysis Training/Courses/Papers?
Scholar 3.1 years ago, created an answer that has been accepted. For A: miRNA corresponds to multiple ensembl gene IDs
Popular Question 3.1 years ago, created a question with more than 1,000 views. For DESeq2 analysis: huge number of outliers and refitting
Centurion 3.2 years ago, created 100 posts.
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: Up-to-date Online RNA Sequence Analysis Training/Courses/Papers?
Commentator 3.4 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 3.5 years ago, created a post with more than 5 votes. For C: Is going back to the wet lab worth it?
Good Answer 3.8 years ago, created an answer that was upvoted at least 5 times. For C: Is going back to the wet lab worth it?
Appreciated 3.8 years ago, created a post with more than 5 votes. For C: Is going back to the wet lab worth it?
Teacher 3.8 years 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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