dwgsim read orientation

[av_d]

Hi everyone,

I want to use dwgsim to simulate solid reads for testing SOLiD denovo2 pipeline(which needs a F3 and another R3 or F5). But I'm little confused with the read orientation of "out.bfast.fq".
Eg, first two reads from my out.bfast.fq is here,

@I_532_32_1_1_0:0:0_0:0:0_0
A2133112101103112111031211
+
1111111111111111111111111
@I_532_32_1_1_0:0:0_0:0:0_0
A3130100331131313012113102
+
1111111111111111111111111

According to dwgsim wiki, the 4th the and 5th field of the read name describing the strand
4. strand end 1 (0 - forward, 1 - reverse)
5. strand end 2 (0 - forward, 1 - reverse)

so my question id how to separate these reads to corresponding F3 and R3(or F5) files ?
Is that first one is F3 and second is R3 ?

[nilshomer]

End one has a position of 532, end two has a position of 32, both are on the reverse strand. In the latest GIT, you will see the "-S" option lets you control the strand relationship between the two. Someone correct me if I am wrong, but F3/R3 (mate pairs) are on the same strand with R3 is 5' of F3 (see http://www.umassmed.edu/uploadedFile...s/Overview.pdf). For F3/F5 (paired ends), they should be on opposite strands with F3 having a lower co-ordinate (see http://sourceforge.net/mailarchive/m...sg_id=27692286). Based on that info, you should be able to figure out from the read names which is which, as well as what settings you used. Maybe we should label the "-S" option with "mate pair mode" or "paired end mode"?

[nilshomer]

I have update the documentation: https://sourceforge.net/apps/mediawi...ome_Simulation

What do you think?

[av_d]

thanks a lot, the wiki page is really helpful.