gistfile1.txt

If you get the error about [error] Barcode out of bounds during cellranger mkfastq:

Have to run bcl2fastq directly like I did in R0063

https://kb.10xgenomics.com/hc/en-us/articles/360038857411--error-Barcode-out-of-bounds-I1-0-14-or-I2-0-16-





bcl2fastq --use-bases-mask=Y28n*,I10n*,I10n*,Y90n* \
            --create-fastq-for-index-reads \
            --minimum-trimmed-read-length=8 \
            --mask-short-adapter-reads=8 \
            --ignore-missing-positions \
            --ignore-missing-controls \
            --ignore-missing-filter \
            --ignore-missing-bcls \
            -r 5 -w 5 \
            -R ${BCLFolder}/${CommonFolderName}/${BCLFolderName}/ \
            --output-dir=${FASTQFolder}/${CommonFolderName}${ExpType}/ \
            --interop-dir=${BCLFolder}/${CommonFolderName}/${BCLFolderName}/InterOp/ \
            --sample-sheet=SampleSheet_cf1df540c23b5.csv
            
            
[Data],,,,,,,,,,,
Lane,Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,I5_Index_ID,index2,Sample_Project,Description,GenomeFolder
2,S0250,,,,,ACCTCGAGCT,,ATCGAACACA,R0063,stuff,