User: mat.lesche

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mat.lesche40
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40
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Location:
Germany
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an hour ago
Joined:
3 years, 11 months ago
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m*********@gmail.com

Posts by mat.lesche

<prev • 52 results • page 2 of 6 • next >
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lfcShrink and factors with multiple levels
... Hello Michael, So far I have used DESeq 2 with betaPrior = T in the DESeq() function but now I'm testing it with betaPrior = False and using lfcShrink either with the coef or contrast parameter (DESeq2 version 1.18.0). I notice a couple of things which I think need clarifcation I used a fairly com ...
deseq2 relevel lfcshrink written 10 months ago by mat.lesche40 • updated 10 months ago by Michael Love19k
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Comment: C: using paired end and single end data in featurecounts
... Or merge in R would work as well. But I would remove the chromosom, start, end, strand and length column in the two dfs. new_df <- merge(table1_df, table2_df, by.x = 'Geneid', by.y = 'Geneid') ...
written 13 months ago by mat.lesche40
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Comment: C: Finding the correct covariate for RNAseq experiment
... Thanks Michael. ...
written 13 months ago by mat.lesche40
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Comment: C: RNA STAR to DESeq2
... You can also have a look at featureCounts (http://bioinf.wehi.edu.au/featureCounts/). It needs a gtf as annotation input, the bam files. You can run it in pe or se. It's pretty nice and produces a table with samples as columns and genes as rows. ...
written 13 months ago by mat.lesche40
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Comment: C: Finding the correct covariate for RNAseq experiment
... Hi James, now there is. Sorry but the Submit was to early. There used to be a preview button. I realised that submit is creating the thread before it was too late. ...
written 13 months ago by mat.lesche40
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Finding the correct covariate for RNAseq experiment
... Hey, I'm running an experiment with two conditions, one is the wildtype and the other is a knock out of a gene. Each sample is from a single mouse and the samples were isolated on different days. Here is an overview Sample GT Sex Date ss11 KO male may s ...
sva deseq2 differential gene expression removebatcheffect() written 13 months ago by mat.lesche40 • updated 13 months ago by Michael Love19k
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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 19 months ago by mat.lesche40
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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 19 months ago by mat.lesche40
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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 19 months ago by mat.lesche40
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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 23 months ago by mat.lesche40

Latest awards to mat.lesche

Popular Question 6 weeks ago, created a question with more than 1,000 views. For DESeq2: with multiple factors and interaction terms won't show all effects
Great Question 18 months ago, created a question with more than 5,000 views. For DESeq2: multiple factors and comparison of a main factor between samples
Great Question 18 months ago, created a question with more than 5,000 views. For DESeq2: with multiple factors and interaction terms won't show all effects
Popular Question 2.4 years ago, created a question with more than 1,000 views. For DESeq2: multiple factors and comparison of a main factor between samples
Popular Question 2.8 years ago, created a question with more than 1,000 views. For DESeq2: multiple factors and comparison of a main factor between samples
Popular Question 2.8 years 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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