Question: how to get counts/TPM/etc. from stringtie?
0
gravatar for dec986
15 months ago by
dec986200
United States
dec986200 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 • 1.3k views
ADD COMMENTlink modified 15 months ago by sanchi.andrea0 • written 15 months ago by dec986200

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 15 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 15 months ago • written 15 months ago by Joe15k

sorry, my mistake!!!

ADD REPLYlink written 15 months ago by sanchi.andrea0
0
gravatar for h.mon
15 months ago by
h.mon28k
Brazil
h.mon28k 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 15 months ago by h.mon28k

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 15 months ago by dec986200
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 15 months ago by h.mon28k

thanks, I've edited the original post

ADD REPLYlink written 15 months ago by dec986200

And how are you trying to run Ballgown?

ADD REPLYlink written 15 months ago by h.mon28k

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

ADD REPLYlink written 15 months ago by dec986200

Hi dec986, sorry to ask but did you manage to get Ballgown to run on the TPMs from StringTie? Thanks

ADD REPLYlink written 7 months ago by rnaseql0
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