Submitting replicate paired-end RNA-seq reads to Tophat

Question

[gwilson9]

I have three replicate paired-end RNA-seq samples that I would like to run through Tophat. I submitted the runs through command line with this code (generic):

tophat -p # genome_index read1_fwd,read2_fwd,read3_fwd read1_rev,read2_rev,read3_rev

and received this error message: Pair #1 name mismatch: read1_fwd vs read2_fwd.

I'm new to this, but it looks like the software thinks that two samples in the first group are intended pairs. Is there a better way that I should submit this job? Thanks for your help!

[Devon Ryan]

It's likely that you put a space somewhere where you shouldn't.

BTW, unless the replicates are technical you shouldn't align them this way.

[gwilson9]

Thanks, you called it. The samples are actually biological replicates. Should they be run separately and merged after aligning?

[GenoMax]

RNA-seq triple replicates