illumina2srf's -use_bases command line argumet

[AijazS]

Hello,

I was wondering if any of you has successfully used illumina2srf's "-use_bases" command line argument? We have a indexed V3 run.

illumina2srf's documentation contains the following, however, doesnt explicitly give an example on how to:
-use_bases <str>
Select which bases make up the forward, index and reverse parts
of the read.

any help is greatly appreciated..

PS: I tried CASAVA's use_bases way of notation 'Y100,Y7,Y100', didnt work though.

[kmcarr]

You need to specify which portion is the index using 'I'. You can also exclude portions of a read with 'N'. I am assuming that although the index read was actually 7 cycles (bases) only the first 6 bases make up the index. In that case the proper string would be:

-use_bases Y100,I6N,Y100

[AijazS]

Thank you for the help kmcarr. It seems to work now.