User: mat.lesche

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mat.lesche10
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Germany
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2 weeks ago
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2 years, 5 months ago
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Posts by mat.lesche

<prev • 36 results • page 1 of 4 • next >
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Comment: C: Increased number of total exons in DEXSeq
... Hey, Have a look at the vignette for DEXSeq. The prepare_annotation script flattens all isoforms from the same gene into a single representation of this gene. During this process it creates exonic bins out of the overlapping exons. For example if you have gene with two isoforms and in isoform A the ...
written 23 days ago by mat.lesche10
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Answer: A: dexseq doesn't identify exons as differential
... Hi Assa, DEXSeq doesn't look for differential expression. The tool is designed to look for a differential usage of single exon bins compared to the usage of all other exon bins in a gene. In your case the gene shows an over expression in EB2 compared to the other condition. Hence the high expressio ...
written 4 weeks ago by mat.lesche10
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counting with htseq script in DEXSeq
... Hey, I'm using DEXSeq on my data for a differential exon usage analysis. My data is paired-end data with the R1 read being on same strand as genomic feature and the R2 read is on the opposite strand. Therefore I set the right setting in the dexseq_count script and set paired = yes as well. I ran th ...
dexseq dexseq_count htseq written 4 weeks ago by mat.lesche10
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Comment: C: Grouping a multifactor design in DESeq2 and accouting for sex
... Thanks for your answer, I really appreciate your help! Because we have another project with 10 comparisons coming up, I'd really like to know at how many comparisons one should do the global corrections? Sorry for all the questions but I always learn something new here. ...
written 5 months ago by mat.lesche10
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Comment: C: Grouping a multifactor design in DESeq2 and accouting for sex
... Hey Michael, Thanks for mentioning the global corrections. I wasn't aware of it. Maybe it would be helpful to add this to the Q&A of the DESeq2 vignette and to refer to the section in the limma vignette? For how many pairwise comparisons do you recommend to do the global corrections? Should one ...
written 5 months ago by mat.lesche10
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Comment: C: Grouping a multifactor design in DESeq2 and accouting for sex
... Hey Michael, I did the PCA again without the sex chromosomes and PC1 went from 50 to 55% and PC2 from 26 to 23%. A plot of genes with the highest variance doesn't show Xist anymore. So I stick to ~sex+group and that's all I can do. ...
written 5 months ago by mat.lesche10
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Comment: C: Grouping a multifactor design in DESeq2 and accouting for sex
... Dear Michael, Thanks for the answer and the confirmation. I have found this thread in which you answered a question regarding pairwise comparison (https://support.bioconductor.org/p/87671/) Does your answer apply to my task as well. I have 28 comparisons because I have 8 pairs. Thanks Mathias ...
written 5 months ago by mat.lesche10
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Comment: C: Grouping a multifactor design in DESeq2 and accouting for sex
... Hey Ryan, Sorry this was my mistake and was not precise. It's not a cell line, it's two different mouse line. One is our standard mouse line, the other one is infected with a disease. ...
written 6 months ago by mat.lesche10
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Grouping a multifactor design in DESeq2 and accouting for sex
... Hello, I want to do an analysis of some mice data with DESeq2. We have a total 24 samples and three factors. Factor one is the genotyp (6 wildtype, 6x knockout 1, 6x knockout2, 6x knockout3) and factor two are two different cell lines (cellA and cellB). Factor three is the sex (male and female ...
deseq2 multiple factor design group written 6 months ago by mat.lesche10 • updated 6 months ago by Michael Love11k
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Comment: C: junction.bed to GTF to use in DEXSeq
... Hello Rahel, there is a new tool which looks and differential usage for exons and junction loci. I'm testing it at them moment because I never finished working on my version. Have a look: http://hartleys.github.io/JunctionSeq/ ...
written 15 months ago by mat.lesche10

Latest awards to mat.lesche

Popular Question 11 months ago, created a question with more than 1,000 views. For DESeq2: multiple factors and comparison of a main factor between samples
Popular Question 15 months ago, created a question with more than 1,000 views. For DESeq2: multiple factors and comparison of a main factor between samples
Popular Question 15 months ago, created a question with more than 1,000 views. For DESeq2: with multiple factors and interaction terms won't show all effects

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