User: maya.kappil

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Posts by maya.kappil

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Comment: C: WGCNA following salmon/DESeq2
... Thanks!  Ah, ok - that makes sense regarding the filtering.  In the code line for the filtering step, the 30 does refer to the sample size of my smallest comparison group.  Counts in low tens for at least this number of samples makes sense, and we do have roughly 50M reads/sample, so I can adjust th ...
written 14 days ago by maya.kappil0
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Comment: C: GC content correction in salmon/deseq2 workflow for single-end RNAseq data
... Great, thanks!   I do have the MultiQC output and will review them for the GC content curves. Right now, I'm doing DGE but would also like to look at differential transcript usage using something like the DRIMSeq package.  ...
written 14 days ago by maya.kappil0
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Comment: C: WGCNA following salmon/DESeq2
... Thanks for the quick response!   ...
written 14 days ago by maya.kappil0
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GC content correction in salmon/deseq2 workflow for single-end RNAseq data
... Hello, My understanding is that it is possible to add a flag for GC content correction when quantifying reads using salmon but that this is really meant for paired-end data.  I'm wondering about what options there are to perform GC content correction on single-end RNA-seq data and to what extent it ...
edaseq deseq2 rna-seq salmon written 14 days ago by maya.kappil0 • updated 14 days ago by Michael Love20k
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WGCNA following salmon/DESeq2
... Hello! If I wanted to conduct WGCNA analysis following a salmon/DESeq2 workflow, would it be appropriate to use the matrix generated after applying the vst function on the dds object? Something akin to the following script: dds<- DESeqDataSetFromTximport(txi, coldata, design = ~ batch + Sex + B ...
deseq2 wgcna salmon written 14 days ago by maya.kappil0 • updated 14 days ago by Peter Langfelder1.6k

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