HISAT2/StringTie/Ballgown for Novel Transcript Isoform Differential Expression
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12 months ago
ra711 • 0

I ran some mm9 data through the HISAT2/StringTie/Ballgown RNA-seq pipeline recently and went through the listed protocol HISAT2/StringTie/Ballgown Protocol. When I used Ballgown, I was not able to identify any novel transcript isoforms as compared with Table 3 from data analyzed in the linked paper. The first thing I tried was to use no filter, but that did not work. I am wondering if there was an issue in how I fed the data into Ballgown in terms of my experimental conditions?

My experiment consists of two experimental levels. The first being a genotype of SMAD4 KO or WT. The second being a treatment of either TGF-beta, BMP, or Ctrl. In total, I have six experimental groups.

Right now I have the following lines of code when trying to analyze the differential expression of the genes and transcripts.

DE by transcript

results_transcripts <- stattest(bg_mm9, feature='transcript', covariate='genotype', adjustvars=c('treatment'), getFC=TRUE, meas='FPKM')


DE by gene

results_genes <- stattest(bg_mm9, feature='gene', covariate='genotype', adjustvars=c('treatment'), getFC=TRUE, meas='FPKM')


I appreciate any advice or guidance. Please let me know if you think there might be any issues besides the experimental grouping/leveling that is preventing me from getting novel transcript isoforms as found in Table 3 of the linked Nature protocol paper. Thank you so much.

RNA-Seq Ballgown HISAT2 StringTie isoform • 508 views
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Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

Thank you!