Hello everyone in the forum, I am current working on RNA-seq, but I am new hand in this field. I want to get gene count and transcript count from each sample in StringTie, but the result does not have that information. I saw galaxy user can extract that info, I am not sure how it works. Here is my command:

stringtie "$bam" \
           -G "$annotation" \
           -o "$raw_dir/stringtie.gtf" \
           -p "$threads" \
           -e \
           -l "$sample" \
           -b "$raw_dir" \
           -f 0.15 \
           -m 200 \
           -a 10 \
           -j 1 \
           -c 2 \
           -g 50 \
           -M 0.95 \
           -A "$raw_dir/abundance.tab"

Here is the result:

abundance.tab  e2t.ctab  e_data.ctab  i2t.ctab  i_data.ctab  stringtie.gtf  t_data.ctab

Thanks~