velvetg ins_length parameter

[Andres_Gomez]

Hi

I have a very simple question regarding the velvetg command, I really don't know what to provide in the ins_length parameter. My Reads were produced with a HiSeq instrument and are 150nt in length, and the average gDNA fragment size: 400-500nt (range from 150bp to 900bp). I noticed that the reads the example in the metavelvet webpage are 100 bp but then they specify 260 as their ins_length parameter. Also if I let velvetg determine ins_length for me , should I still write that argument in script and just complement with auto?

I'd really appreciate your help, as this is not straight forward from the manual or from web-page and it's the first time I deal with this data.

Thanks

Andy

[chkuo]

The 'ins_length' parameter is for specifying the insert size, so you can use a value between 400 and 500. An easier way is to just leave this out in the initial runs. Velvet will estimate the insert size and report it in the log file. After you get this estimate, you can then specify it in the next run.