How to quantify lncRNA using strintgie？

[qingzengLi]

I'm trying to use stringtie to quantify lncRNA data, the lncRNA gtf file is generated from stringtie. I find that the expression matrix is different from the matrix generated by featureCounts.Which software is more accurate? Here are the comments

stringtie -e -G lncRNA.gtf -p 8 -A ${id}_abundance.txt -o s${id}.gtf 03.align/*.bam
python prepDE.py -i sample-gtf.txt -g lncRNA-count.csv -t lncRNA-transcript-count.csv

featureCounts -T 20 -p -B -C -f -t transcript -g transcript_id -o all_features.txt -a lncRNA.gtf 03.align/*.bam