Question: how to get counts/TPM/etc. from stringtie?
0
gravatar for dec986
7 months ago by
dec986160
United States
dec986160 wrote:

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

rna-seq • 737 views
ADD COMMENTlink modified 7 months ago by sanchi.andrea0 • written 7 months ago by dec986160

Hi h.mon, do you know if to run that python script I have to use a txt file or if is even possible to use the output.gtf file from stringtie?

ADD REPLYlink written 7 months ago by sanchi.andrea0

Please stop posting comments as new answers sanchi.andrea

Use the ADD REPLY/ADD COMMENT buttons below the post instead.

ADD REPLYlink modified 7 months ago • written 7 months ago by jrj.healey11k

sorry, my mistake!!!

ADD REPLYlink written 7 months ago by sanchi.andrea0
0
gravatar for h.mon
7 months ago by
h.mon24k
Brazil
h.mon24k wrote:

What version of StringTie are you using? Since version 1.1.0 TPMs should already be part of the output. If you want counts, you can use the prepDE.py script, see the section Using StringTie with DESeq2 and edgeR from the StringTie manual.

ADD COMMENTlink written 7 months ago by h.mon24k

hi @h.mon,

I'm trying to make input for ballgown, and ballgown, and I have TPM info in the GTF files, but the problem is that ballgown doesn't see them.

ADD REPLYlink written 7 months ago by dec986160
1

Please edit your post to include the commands you used so far. Do not forget to use the code button to properly format the code bits.

ADD REPLYlink written 7 months ago by h.mon24k

thanks, I've edited the original post

ADD REPLYlink written 7 months ago by dec986160

And how are you trying to run Ballgown?

ADD REPLYlink written 7 months ago by h.mon24k

I've edited the original question to show how I'm running ballgown

ADD REPLYlink written 7 months ago by dec986160
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