I've recently obtained one lane PE100 Hiseq data from a highly biased library due to recstriction enzyme overhangs in reads (GBS protocol). Quality values are low for the first 10 cycles, probably due to the non-balance composition due to in-line barcodes.
The lab that normally runs these libraries for us uses a separate PhiX lane which is set as control in the HCS software as described here:technote_phixcontrolv3.pdf.
Is it possible to reprocess the BCL files using the data from another lane (with a non-biased composition) as a control to correct for phasing errors that occured in the GBS-lane? Will this have the same effect as setting a different lane as control prior to the run?
The lab that normally runs these libraries for us uses a separate PhiX lane which is set as control in the HCS software as described here:technote_phixcontrolv3.pdf.
Is it possible to reprocess the BCL files using the data from another lane (with a non-biased composition) as a control to correct for phasing errors that occured in the GBS-lane? Will this have the same effect as setting a different lane as control prior to the run?
Comment