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===Edit SampleSheet.csv=== *Prior to running bcl2fastq, you must first make a few edits to the SampleSheet.csv file provided in the downloaded folder (this is in case there are both dual-indexed and single-indexed libraries in the same run). Let's say that the original SampleSheet.csv file is as follows with BS libraries being dual-indexed and CW libraries being single-indexed: [Header],,,,,,,,, IEMFileVersion,4,,,,,,,, Investigator Name,Chris and Brandon,,,,,,,, Experiment Name,2015 05 12 Miseq,,,,,,,, Date,5/12/2015,,,,,,,, Workflow,GenerateFASTQ,,,,,,,, Application,FASTQ Only,,,,,,,, Assay,Nextera XT v2 Set A,,,,,,,, Description,2015 05 12 miseq,,,,,,,, Chemistry,Amplicon,,,,,,,, ,,,,,,,,, [Reads],,,,,,,,, 151,,,,,,,,, ,,,,,,,,, [Settings],,,,,,,,, ReverseComplement,0,,,,,,,, ,,,,,,,,, [Data],,,,,,,,, Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,I5_Index_ID,index2,Sample_Project,Description BS-4.23.15_BA8_nuclei_S502/N701,,,,N701,TAAGGCGA,S502,CTCTCTAT,, BS-4.23.15_BA8_nuclei_S502/N702,,,,N702,CGTACTAG,S502,CTCTCTAT,, BS-4.23.15_BA8_nuclei_S502/N703,,,,N703,AGGCAGAA,S502,CTCTCTAT,, BS-4.23.15_BA8_nuclei_S502/N704,,,,N704,TCCTGAGC,S502,CTCTCTAT,, BS-4.23.15_BA8_nuclei_S502/N705,,,,N705,GGACTCCT,S502,CTCTCTAT,, CW-PPCap-HP-Apr21-12,,,,CW1,CTTGTANN,CW1.1,NNNNNNNN,, CW-PPCap_2A_H-May7-21,,,,CW2,CAACCCNN,CW1.2,NNNNNNNN,, CW-PPCap_2B_P-May7-28,,,,CW3,AGGTGCNN,CW1.3,NNNNNNNN,, CW-PPCap_2C_HP-May7-2,,,,CW4,CGATGTNN,CW1.4,NNNNNNNN,, CW-PPCap_2C-Mar13-36,,,,CW5,CAAGCANN,CW1.5,NNNNNNNN,, CW-PPCap_2D-Mar13-43,,,,CW6,AGTGCCNN,CW1.6,NNNNNNNN,, *If we were interested in the dual-indexed BS libraries, we would simply remove the CW lines and proceed on to the next step. *However, say we are interested in the CW single indexed reads with barcodes found in index1 and only being 6 bases long. In order to demultiplex these CW libraries, we must consequently make the following changes to the SampleSheet.csv file (with all other lines above being constant): [Data],,,,,,,,, Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,I5_Index_ID,index2,Sample_Project,Description CW-PPCap-HP-Apr21-12,,,,CW1,CTTGTA,CW1.1,,, CW-PPCap_2A_H-May7-21,,,,CW2,CAACCC,CW1.2,,, CW-PPCap_2B_P-May7-28,,,,CW3,AGGTGC,CW1.3,,, CW-PPCap_2C_HP-May7-2,,,,CW4,CGATGT,CW1.4,,, CW-PPCap_2C-Mar13-36,,,,CW5,CAAGCA,CW1.5,,, CW-PPCap_2D-Mar13-43,,,,CW6,AGTGCC,CW1.6,,, *Once the SampleSheet.csv has been updated accordingly, you can then move forward with actually running the bcl2fastq program. '''Note: Make sure that the RunInfo.xml file is in the current running directory, as bcl2fastq will produce an error if it is not. Since we are running within the original downloaded folder from basespace, this is not an issue.'''
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