User: Nancy

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Nancy0
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Posts by Nancy

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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 18 days ago by Nancy0 • updated 18 days ago by Michael Love19k
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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 5 months ago by Nancy0
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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 8 months ago by Nancy0

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