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Posts by mnandita
Comment: C: DESeq2 vs Ballgown results
... Hi Alyssa, Even with transcript-level DE analysis using Ballgown, we haven't had much success- many of the transcripts identified as D.E. from ballgown, did not show a clear D.E. when visualizing the raw bam files in IGV. I've described an example in issue #2 here https://support.bioconductor.org/ ...
... Our lab has tried to adopt the Pertea et al protocol (https://www.nature.com/articles/nprot.2016.095]) to evaluate Differential Gene Expression in mouse (one single tissue)- the set up is with 3 or 4 replicates per treatment, comparing treated vs control. We have observed a few issues we are unable ...
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