I'm using hisat2 for aligning reads to genome. stringtie for quantification steps. Used stringtie --merge for assembling all samples gtf. The stringtie_merged.gtf doesn't have any FPKM, TPM or coverage columns which are present in sample gtf files. Is there a way to get all those columns with stringtie --merge?
And why some transcripts which are present in sample gtf files missing in stringtie_merged.gtf file?
Thank you !!