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To extract all the barcode sequences UNASSIGNED by the LifeTech software from an .xsq file, use:
extractBCfromXSQ <input.xsq> > bc.csfasta 2> bc_QV.qual
To extract all the unassigned F3, or F5-RNA sequences from an xsq file, use:
extractF3fromXSQ <input.xsq> > f3.csfasta 2> f3_QV.qual
or
extractF5fromXSQ <input.xsq> > f5.csfasta 2> f5_QV.qual
(note that these are all just scripts that call other scripts to do all this - pretty easy to extract anything from an hdf file. You sometimes have to use hdfview to see exactly what the tables in the .xsq file are called, then use h5dump to pull it out).
<input.xsq> should be the raw, final .xsq file for the lane, not the _Unassigned.xsq residual file generated after convertFromXSQ.sh.