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)