Tophat - processing several files fastq

[marb]

Hello.
I use data from Illumina GA IIx procesed by Casava to fastq files.
There is several fastq files in each lane.
How to processing that all files at same time by tophat?
I tried type:

tophat reference_genom_path ./*.gz --output-dir output_dir_path

but I'm affraid that it's not good way

[gringer]

you need to separate by comma rather than by space (the '*' expands files by spaces). I've been doing this using the printf command, but there may be other better ways:

tophat reference_genom_path $(printf "%s," ./*.gz | sed 's/,$/\n/') --output-dir output_dir_path

[marb]

In my opinion your solution is very good. It's works!!!
Thank you very much for help.

[ataheri]

accepted_hits.bam file

Just wondering whether we need to have accepted_hits.bam file for each pair or having just one accepted_hits.bam would be enough for further analysis in cufflinks for multiple paired-end samples.