User: VHahaut
VHahaut • 1.1k
- Reputation:
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- Belgium
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- Vincent_Hahaut
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- 6 days, 13 hours ago
- Joined:
- 5 years, 1 month ago
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Posts by VHahaut
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... 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 ...
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... 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 ...
written 8 months ago by
VHahaut • 1.1k
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... 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 ...
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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 2.2 years 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 2.3 years 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 2.6 years 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 2.8 years ago by
VHahaut • 1.1k
0
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... What are those barcodes exactly, unique molecular identifiers? ...
written 2.8 years 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 2.8 years ago by
VHahaut • 1.1k
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For Conversion sheep/mammal ID to human for GSEA
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For MA plots DESeq: strange MA plots
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For A: miRNA corresponds to multiple ensembl gene IDs
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For Conversion sheep/mammal ID to human for GSEA
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For Conversion sheep/mammal ID to human for GSEA
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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 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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2.9 years ago,
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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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