tophat junctions.bed

[MerFer]

Dear TopHat users,

I have 51bp-long, paired-end reads. I'm using TopHat v1.0.13, with Bowtie 0.11.3, on a Linux computer with x86_64 architecture.
I run TopHat with the following parameters:

tophat -G /home/../Homo_sapiens.GRCh37.58VN.gff -r 80 --no-novel-juncs -a 8 -m 0 -I 1000000 -g 100 -o ~/tophat_sj --segment-mismatches 2 --segment-length 25 --max-segment-intron 1000000 /....../hg18 /......./s_1_1.fastq /...../s_1_2.fastq

Here is an example from my GFF file:

chr11 protein_coding gene 127926 139099 . - . ID=ENSG00000230724;Name=AC069287.3

chr11 protein_coding mRNA 130207 131297 . - . ID=ENST00000427071;Name=AC069287.3;Parent=ENSG00000230724
chr11 protein_coding exon 131120 131297 . - . ID=ENST00000427071.1;Name=AC069287.3;Parent=ENST00000427071
chr11 protein_coding exon 130207 131087 . - . ID=ENST00000427071.2;Name=AC069287.3;Parent=ENST00000427071
chr11 protein_coding mRNA 129736 139099 . - . ID=ENST00000435244;Name=AC069287.3;Parent=ENSG00000230724
chr11 protein_coding exon 138956 139099 . - . ID=ENST00000435244.1;Name=AC069287.3;Parent=ENST00000435244
chr11 protein_coding exon 138047 138111 . - . ID=ENST00000435244.2;Name=AC069287.3;Parent=ENST00000435244

But the results in the output 'junctions.bed' file confused me. There were only 13 lines in the junctions.bed file. Do you have any idea, what could it be wrong?

Here ist the result in the output 'junctions.bed' file.

track name=junctions description="TopHat junctions"
chr19 12921175 12923905 JUNC00000001 3 + 12921175 12923905 255,0,0 2 43,9 0,2721
chr17 11964 13953 JUNC00000002 1 - 11964 13953 255,0,0 2 17,33 0,1956
chr17 13975 22361 JUNC00000003 2 - 13975 22361 255,0,0 2 20,34 0,8352
chr17 63676 65480 JUNC00000004 6 - 63676 65480 255,0,0 2 38,36 0,1768
chr17 65562 69456 JUNC00000005 6 - 65562 69456 255,0,0 2 31,43 0,3851
chr17 69483 96937 JUNC00000006 9 - 69483 96937 255,0,0 2 44,36 0,27418
chr17 97032 131597 JUNC00000007 4 - 97032 131597 255,0,0 2 44,39 0,34526
chr17 131603 169252 JUNC00000008 17 - 131603 169252 255,0,0 2 42,42 0,37607
chr17 169298 171106 JUNC00000009 11 - 169298 171106 255,0,0 2 42,44 0,1764
chr17 171164 177295 JUNC00000010 5 - 171164 177295 255,0,0 2 42,38 0,6093
chr17 177335 183564 JUNC00000011 1 - 177335 183564 255,0,0 2 35,15 0,6214
chr1 1551952 1552467 JUNC00000012 2 + 1551952 1552467 255,0,0 2 42,10 0,505

Thanks