Oh yes I can check that.

#! /bin/bash
strp=/home/xxx/softwares/stringtie-2.1.4
gtf=/home/xxx/Documents/sss/genome.gtf
thr=40

find ./ -iname "*.bam" >li1
cat li1|while read e
do
        base_name=$(basename $e .bam)
        ${strp}/stringtie -p ${thr} -G ${gtf} -o ${base_name}.gtf -l ${base_name} $e
done

find ./ -iname "*.gtf" >li2.list

${strp}/stringtie -p ${thr} --merge -G ${gtf} -o stringtie_merged.gtf li2.list

cat li1|while read a
do
        base_nam=$(basename $a .bam)
        ${strp}/stringtie -e -p ${thr} -G stringtie_merged.gtf -o ${base_nam}.re.gtf $a
done
find ./ -iname "*.re.gtf"|while read i
do
        aa=$(basename $i .re.gtf)
        printf "$aa\t$i\n"
done >reli2.list #for each path, add SRR accession and space at start of line

python ${strp}/prepDE.py -i reli2.list

This was the total script I have used though.