Created
October 1, 2025 18:22
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| BCL Convert sample sheet and bcl2fastq command for ATAC data (pasted below). | |
| Example BCL Convert Sample Sheet: | |
| [Header],, | |
| FileFormatVersion,2, | |
| RunName,20240307_HH_AT209_Deep_ATAC, | |
| InstrumentPlatform,NextSeq500/550, | |
| InstrumentType,NextSeq550, | |
| ,, | |
| [Reads],, | |
| Read1Cycles,50, | |
| Read2Cycles,50, | |
| Index1Cycles,8, | |
| Index2Cycles,60, | |
| ,, | |
| [BCLConvert_Settings],, | |
| OverrideCycles,Y50;I8;U60;Y50, | |
| CreateFastqForIndexReads,1, | |
| TrimUMI,0, | |
| ,, | |
| [BCLConvert_Data],, | |
| Sample_ID,index,index2 | |
| AT209_fresh_T0_QB,TAAGGCGA, | |
| AT209_frozen_T0_QB,CGTACTAG, | |
| AT209_fresh_T0_HH,AGGCAGAA, | |
| AT209_frozen_T0_HH,TCCTGAGC, | |
| AT209_fresh_24h,GGACTCCT, | |
| AT209_frozen_24h,TAGGCATG, | |
| AT209_fresh_48h,CTCTCTAC, | |
| AT209_frozen_48h,CAGAGAGG, | |
| AT209_fresh_72h,GCTACGCT, | |
| AT209_frozen_72h,CGAGGCTG, | |
| Example bcl2fastq Command: | |
| bcl2fastq --input-dir BaseCalls --runfolder-dir rRunfolder --sample-sheet SampleSheet.csv --output-dir Demultiplexed_Data --interop-dir Demultiplexed_Data/interop_path --use-bases-mask y*,I8n*,y*,y* -p 20 --ignore-missing-positions --ignore-missing-filter --ignore-missing-bcls --create-fastq-for-index-reads | |
| Run setup is: 51-8-60-51 | |
| Our demux output generated: R1, I1,R2, R3 | |
| R1 is Read1 | |
| I1 is i7 index sequence used for the demux | |
| R2 associates with the i5 index read (Based on the requirement rename this file to I2) | |
| R3 is Read2 |
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