Tophat Junction reads are very low comapred to ERANGE

[repinementer]

Does any one know why the number of junction reads of TopHat (117410) are very less compared to ERNAGE. It should be more than ERANGE I suppose ?

And the genomic reds number is more than the original reads? (32233301)

I ran Illumina solexa single end rnaseq reads

BLAT+ERANGE
Samples No. Reads Genomic reads Genomic reads Junction reads
Adipose 27752231 17.6 M (unique) 4.8 M (non-unique) 1.4MB


BOWTIE+TOPHAT

Samples No. Reads Genomic reads Junction reads
Adipose 27752231 32233301 117410

[Thomas Doktor]

Could you give us a bit more information about how you count the number of reads?