I am hoping to get a bit more help in relation to the issue of MSTRG in place of transcriptname and geneID. I have followed the comments as best as I can from: Stringtie does not always add gene_name? #113
I have run each single gtf from stringtie as input into gffcompare ( annotation mode) and generated sample.annotated.gtf files using this code:
gffcompare -r path/to/reference/gtf/ -o label original_gtf_stringtie
I then used these annotated.gtf files as input into ballgown (in place of the original gtf output from stringtie, but with the original ballgown tables) and the transcript expression table still has lots of MSTRG ID instead of transcriptnames.
There isnt much information on gffcompare annotation mode to understand how this works and what the output file should look like and how I can check this has worked as expected. I am supposed to re-run stringtie with the annotated.gtf files?
What am I doing wrong? I would be super grateful for any help, I am unable to progress with my workflow.
Hi there,
I am hoping to get a bit more help in relation to the issue of MSTRG in place of transcriptname and geneID. I have followed the comments as best as I can from: Stringtie does not always add gene_name? #113
I have run each single gtf from stringtie as input into gffcompare ( annotation mode) and generated sample.annotated.gtf files using this code: gffcompare -r path/to/reference/gtf/ -o label original_gtf_stringtie
I then used these annotated.gtf files as input into ballgown (in place of the original gtf output from stringtie, but with the original ballgown tables) and the transcript expression table still has lots of MSTRG ID instead of transcriptnames.
There isnt much information on gffcompare annotation mode to understand how this works and what the output file should look like and how I can check this has worked as expected. I am supposed to re-run stringtie with the annotated.gtf files?
What am I doing wrong? I would be super grateful for any help, I am unable to progress with my workflow.
thanks
Lauren :)