a question about tophat and cufflinks

[camelbbs]

hi,

I have some questions about using tophat and cufflinks.

1. I want to ask if these tools can extract all transcript level from my input fastq sequence, like the microarray matrix.

2. I have downloaded a geo fastq sequence, size 1G, and use

tophat mm9 SRRXXX.fastq

got a warning like :

Warning: junction database is empty!

And the result .bam file only have 270k.

then I use cufflinks accepted_hits.bam

got result in transcripts.gtf, only have 10 rows.

So what is this problem?

Thanks so much.