I have analysed a few studies from the species Schistosoma mansoni using HISAT2 and Stringtie, mostly with no problems, using the genome and corresponding annotations retrieved from the same site (http://parasite.wormbase.org/Schistosoma_mansoni_prjea36577/Info/Index). I have seen people discuss this same problem due to getting the genome and annotations from different sites (ie they aren't compatible), but this surely isn't the case here.
Studies analysed are from 2012-2015. Attempted analyses of two more recent studies (both 2016) have resulted in the columns; Coverage, FPKM and TPM all containing 0s in every single row.
I only want to obtain FPKMs for existing genes, so I am using Stringtie with no new transcript assembly. My command is as follows;
stringtie -p 8 -G ../SmanAnnos.gtf -e S24_B1.bam -A S24_B1.tab
I'm a bit of a noob to Stringtie, so the more simple the explanation the better. Many thanks.