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Tag: dseq2
Batch effect normalization
Batch effect normalization 0 hello people! my rna seq data has been sequenced in 5 batches. upon applying MW stats, i found signifcance for orimary aligned readcounts between batches. since the data is for severity, i compared mild of batch 1 with mild of another batch and likewise for mod…
CombatSeq on a large dataset before running DSeq2 on a very small subset?
CombatSeq on a large dataset before running DSeq2 on a very small subset? 0 I have an RNA-Seq counting table containing approximately 400 patients with similar diseases, and these patients were sequenced in four batches. (Among the batches, we have noticed a strong effect in batch 4 and a “moderate”…
INSTALLING Dseq2 via conda
INSTALLING Dseq2 via conda 0 Hello, I am installing Dseq2 software for RNA seq analysis via conda but it says UnsatisfiableError: The following specifications were found to be incompatible with your system: feature:/linux-64::__glibc==2.35=0 bioconductor-deseq2 -> libgcc-ng[version=’>=10.3.0′] -> __glibc[version=’>=2.17′] Your installed version is: 2.35 I have created a new environment and…
Normalization and differential analysis in ATAC-seq data
Normalization and differential analysis in ATAC-seq data 2 Hello everyone! I would like to know if someone had experiences with normalization and differential expression on ATAC-seq data. After using MACS2 for the peak calling, how can we use Dseq2 or EdgeR on these datas? Someone try this? What is the…