User: Nancy

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Nancy10
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Posts by Nancy

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DESeq2 ratio of small p-values plot
... While analyzing RNA-seq data for differentially expressed genes, I was wondering if it would be appropriate to use the "ratio of small p values vs mean normalized count" diagnostic plot, to decide upon a cutoff of counts to consider as "minimum counts" to shortlist genes for further analysis. Addit ...
deseq2 diagnostic plots written 11 months ago by Nancy10 • updated 11 months ago by Michael Love26k
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Usage of prepDE.py with stringtie and deseq2
...  I have been following the usage of prepDE.py script to convert stringtie quantifications to counts to input to DESeq2, exactly as described here: [http://ccb.jhu.edu/software/stringtie/index.shtml?t=manual#deseq] We typically run Stringtie in the simple reference-based mode (using the –eB argument ...
deseq2 stringtie prepde written 13 months ago by Nancy10 • updated 13 months ago by Michael Love26k
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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/ ...
written 18 months ago by Nancy10
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RNA-seq with hisat2+stringtie+ballgown
... 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 ...
rnaseq ballgown stringtie hisat2 written 21 months ago by Nancy10

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