transcript count after string tie merge
Entering edit mode
4.4 years ago
rthapa ▴ 60

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


python -i sample1.txt

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

Could anyone suggest me what might have gone wrong? Thanks

rna-seq stringtie • 2.7k views
Entering edit mode
4.4 years ago

stringtie --merge is only supposed to be used to create a consensus GTF reference from multiple GTF files. The idea of doing this is that it helps with downstream analyses. For example: how could you accurately do differential expression analysis on multiple samples, each with different transcript co-ordinates in their respective GTF files? With a consensus GTF, this becomes a whole lot easier.

Once you generate the consensus GTF, you can then re-estimate abundances by re-running StringTie with the -e command-line parameter on all of your samples.

Take a look at the very helpful manual: StringTie Transcript assembly and quantification for RNA-Seq

Cross-posting: transcript count after string tie merge


Entering edit mode

this was very helpful. Thank you!


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