Hi EveryOne, I am new to RNA-seq data analysis, now am trying to compare different quantifiers, Stringtie, featurecounts and HTSeq . I have some questions, i am really happy if someone helps me.
I have removed the genes which are have <99 read counts. Is that ok or should i go for 9?
When i have removed <99 read counts genes i got 11802 genes from featurecounts , 11305 from HTSeq and 16502 from Stringtie.(Note : In stringtie, I have used PrepDE.py for gene read counts conversion from FPKM values). Why stringtie gave more genes ? Is Stringtie results are genes or transcripts?
I have used ensembl GRCh38 fasta and gtf files.