Negative coverage values (version 2.1.3b)

[junghoon-shin]

I've noticed some transcripts have negative coverage values in the output gtf file from StringTie 2.1.3b. Can this be a bug?

Below is my script.

while read bam
do
        stringtie "$bam" \
               -G reference.gtf \
               -o "$bam".first.gtf
done < bam_list.txt

ls *.first.gtf > stringtie_first_gtf_list.txt

stringtie --merge \
        -p 20 \
        -G reference.gtf \
        -o stringtie_merged.gtf \
        stringtie_first_gtf_list.txt

while read bam
do
        mkdir "$bam"_second
        stringtie "$bam" \
                -A "$bam"_second/"$bam"_gene_abundance.tsv \
                -B \
                -e \
                -G stringtie_merged.gtf \
                -o "$bam"_second/"$bam".second.gtf
done < bam_list.txt