a question about merge bam files

[camelbbs]

I want to ask a question about bam files.

I have 2 sequencing library in a same sample, and get 2 fastq files, the length of reads are 50bp and 36bp separately.
When I do tophat, because I need to specify the -r, I cannot merge the two fastq files. But after I got the accepted.bam files, can I merge them (bam files) with the samtools merge?

I need to do cufflinks and cuffdiff using the merged bam files.

thanks everyone.

[kentnf]

I have the same question.

[ECO]

This question was crossposted here: http://seqanswers.com/forums/showthread.php?t=14980