No coverage in .tmap file

[zoewardnz]

Hi, I am running stringtie merge and then gffcompare: gffcompare -r gencode.gtf -G -o gff stringtie_merged.gtf When I look at the gff.stringtie_merged.gtf.tmap all values are zero for FPKM,TPM, and coverage for all transcripts??

[gpertea]

Is there such coverage data in the given GTF: stringtie_merged.gtf ?

gffcompare does not compute coverage, it only fetches the existing coverage values from the input GTF, which are going to be there only if that GTF comes from a straight (regular) run of StringTie or Cufflinks on some sample alignment data. However stringtie --merge does not produce a file with such coverage data.. Typically that merge step is followed by a coverage estimation step for each sample (using the -e option of stringtie) -- and only that output GTF will have the coverage data.