transcript count after string tie merge

[rthapa]

Hi, I am trying to get transcript count with stringtie merge command. I have set of gtf output, when I checked the transcript count of individual gtf files, I got some values of transcript count but when I used strigtie merge command to merge all the stringtie files, I got merged output file but the transcript count are all 0 for all the transcripts. I used the following command lines:

stringtie --merge -p 8 -o stringtie_mergedA.gtf stringtieoutputgtf.txt

where stringtieoutputgtf.txt looks like:
/scratch/user/rthapa/RNA-seq/stringtieS1Routput.gtf
/scratch/user/rthapa/RNA-seq/stringtieS2Routput.gtf
/scratch/user/rthapa/RNA-seq/stringtieS3Routput.gtf
/scratch/user/rthapa/RNA-seq/stringtieS4Routput.gtf
/scratch/user/rthapa/RNA-seq/stringtieS5Routput.gtf
/scratch/user/rthapa/RNA-seq/stringtieoutputS6R.gtf
/scratch/user/rthapa/RNA-seq/stringtieoutputS7R.gtf
/scratch/user/rthapa/RNA-seq/stringtieoutputS8R.gtf
/scratch/user/rthapa/RNA-seq/stringtieoutputS9R.gtf
/scratch/user/rthapa/RNA-seq/stringtieoutputS10R.gtf

python prepDE.py -i sample1.txt

sample1.txt looks like stringtie_mergedA.gtf /scratch/user/rthapa/RNA-seq/stringtie_mergedA.gtf

Could you suggest me what could be the problem here?

[sdriscoll]

I'm interpreting your meaning of "transcript counts" to be the expression levels of transcripts. You're correct that those do appear in the individual assemblies however after merging, since the assembly changes, those values are dropped since you built a single annotation from several samples - you cannot also summarize the expression of those transcripts from all samples into a single annotation that may not exactly match any of them.

If I'm not mistaken you need to take the final merged GTF and then re-run stringtie with quantification only mode (using -e). You'd specify your merged GTF with -G. That should give you expression values for your merged assembly.