hello,

I'm running stringtie to quantify transcripts on single-end RNA-Seq. how can I get stringtie to output more than FPKM and cov? Ballgown, which is meant for differential expression, gives options for inputting data in format "rcount", "ucount", "mrcount", "cov", "cov_sd", "mcov","mcov_sd", or "FPKM". but all I can see how to put out is 'FPKM' & 'cov' which come in standard. I don't see how to do this from the help menu. It appears that stringtie can do this, because Ballgown says that it can take this input. I just can't find out how to make it.

my stringtie commands were run like:

stringtie sorted.bam -G /illumina/runs/RNASeq/Gencode27/gencode.v27.annotation.gtf -A stringtie.tab -o stringtie.gtf -T 1 -eBt

and ballgown is run

library(ballgown)
library(RSkittleBrewer)
library(genefilter)
library(dplyr)
library(devtools)
samples <- c("/dir/A","dir/B","dir/C", "dir/D")
bg = ballgown(samples=samples, meas="all")
bg_filtered <- subset(bg, "rowVars(texpr(bg)) > 1", genomesubset = TRUE)
rm(bg)
pData(bg_filtered) = data.frame(id=sampleNames(bg_filtered), group=c(rep(0,2), rep(1,2)))
results_transcripts = stattest(bg_filtered, feature="transcript", meas="FPKM", getFC = TRUE, covariate="group")
results_transcripts <- data.frame(transcriptNames=transcriptNames(bg_filtered), results_transcripts)
results_transcripts <- results_transcripts[order(results_transcripts$qval),]#sort by qval
write.table(file = "ballgown_output/J1_and_J2яEarlyяH1_H2_and_H5_vs_control.tsv", results_transcripts, sep="\t", quote=FALSE)

-Dave