Running tophat sample data, please help

[joeyxiao1984]

I'm new to tophat analysis, and trying to do some practice with data from NCBI to mm9 index.

I was following http://www.broadinstitute.org/softwa...hrough_example

and running tophat seems to be ok, but the result is accepted_hits.bam instead of accepted_hits.sam, another thing I noticed that accepted_hits.bam is less than 1MB, and there is another file called unmapped.bam which is more than 2GB.

Since I'm following the steps exactly, can anyone tell me what the problem is? Thanks a lot and any suggestion is greatly appreciated.

[joeyxiao1984]

Something differences are that I downloaded the new data file with SRA extension, I manually converted to fastq file, and I used tophat2 and used the new index file .bt2 instead of the old ones.