I have used BBMap for RNA-seq reads mapping. After mapping, i tried HTSeq, FeatureCounts and STRINGtie for quantification. But, i didn't get any results from featureCounts and HTSeq (readcount for all genes 0), STRINGtie showing that " your gtf file doesn't matched with your reference genome ". The strange is the same reference genome and annotation gtf files were tried with STAR aligner, but i didn't get any errors , working fine. Any suggestions, Thanks .
Here is the command used for BBMap :
./bbmap.sh threads=16 in1=/home/1.fastq in2=/home/2.fastq out=/home/output.sam ref=/home/Homo_sapiens.GRCh38.77.fa nodisk