bfast bgeneratereads for paired ends

[sdvie]

Dear all,

I was trying out the bgeneratereads utility just now, trying to obtain reads that mimic a paired-end experiment in colorspace with 50 and 25 bp read pairs.
The specification file I generated looks like this:

0 0 0 3 1 50 0 25 100

however, the output is one single file in a format that resembles the solid2fastq output for paired end reads inputting both reads files.
Also, I am not sure about what is meant by "read length" (field 6) vs. "paired end length" (field 8). I interpret it as "read length" = length of the first read of the pair and "paired end length" = length of the second read of the pair. Correct?

Is it possible to somehow generate the two reads of each pair in separate files? (In order to proceed with the bfast match/bfast bwaaln combination?)

Many thanks in advance for suggestions.

cheers,
Sophia

[sdvie]

to - in part - answer my own question, the specification file must look like this:

0 0 0 3 1 50 1 25 100

the field for paired end must be 1 (in that point the manual is wrong, saying "paired end" 0: true, 1: false - in fact it is the other way round).

cheers,
Sophia

[nilshomer]

This utility is not supported within BFAST. Try the "dwgsim" tool within DNAA (http://dnaa.sf.net), which should be more friendly.