What's the difference between the Solid F5-P2 and R3 end data?

[ryuky]

Sure, R3 is for a mate-pair run and F5-P2 is for a paired-end run, but for making the fastq files this doesn't matter. Right?

yeah, I have read this script,
first I think the script will translate the mate-end R3 to the complementary trand because F3 and R3 come from the same strand and next step we must use the paired-end, which come from different strand, to do BWA aln. But I think this script don't do this.

[kopi-o]

Sure, R3 is for a mate-pair run and F5-P2 is for a paired-end run, but for making the fastq files this doesn't matter. Right?

[ryuky]

You should be able to just change all occurrences of "F5-P2" to "R3".

I think the F5-P2" and "R3" are totally different! One comes from the same +strand with the F3 file(R3) and the other come from the reverse strand.
you could see the ABI's protocol for construct the mate-pair library

[kopi-o]

You should be able to just change all occurrences of "F5-P2" to "R3".

[ryuky]

What's the difference between the Solid F5-P2 and R3 end data?
In order to use the BWA solid2fastq.pl I must have the R3 ended data, so how can I just transform the F5-P2 to R3?