Hi. I have a time series RNASEQ experiment with 2 controls and 3 treated samples for each time point.
sample time condition...
12 results in 0.0030 seconds.
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DESEQ2 Desing formula time series experiments with sham controls.
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Should discordant pairs be used for counting/DGE?
Hello everyone,
I am using the STAR aligner, which reports discordant pair alignments in a seperate BAM file. Using my workflow I want... -
DESeq2 with different replicates
There are 104 samples, 38 samples are treated, 66 samples are control. The following script was used to do DGE analysis. But there is no any different... -
RSEM with HISAT2
Hello guys,
I have RNA-sequencing data of around 250 patients with leukaemia.
I have built up a basic pipeline using HISAT2 as... -
48 Replicate RNA-Seq Study Points to Requirements for DGE
Unfortunately, we estimate ~80% of those doing DGE use only 3 replicates. At least 6 replicates should be used to account for variability, bad replicates... -
Why use RNA-SEQ app for DGE rather than t-test?
Hello all, please excuse this rather naïve question but why should I use an RNA-SEQ specific application (such as edgeR, DESeq, etc.) on counts rather... -
mRNA-seq experiment: how to deal with technical replicates
Dear all,
I would like to have our opinion on how to deal with technical replicates in a mRNA-seq experiment for DGE analysis. I saw multiple... -
Are unequal pool sizes for RNA-seq acceptable?
Background:
I want to find differentially expressed genes between wild type (WT) and knockout (KO) mice of mixed background using RNA-seq (Illumina... -
Normalization / Transformation of DE data with a de novo assembly
Hello,
I have a question regarding transformation and/or normalization as it applies to analysis of differential expression (DE) for a... -
Quetion about DGE
Dear All,
Would some one please tell me what are distinct clean tags and Unambiguous tags? And what's the difference?
Thanks!
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Displaying DGE (bed-files) with Integrative Genomics Viewer
I have digital gene expression data in bed-format.
One type of file would be bed-files where each entry corresponds to one sequenced tag.... -
MAQ and short read length (DGE)
We are currently looking into the viability of Digital Gene Expression (DGE) or mRNA-seq as a possible replacement for expression microarrays in our breast...
