I have a question regarding the usage of bcl2fastq for an Agilent panel. The manufacture suggests in this guide to use the parameter "---use-bases-mask" with the specification Y*,I8,Y10,Y*.
Bcl2fastq throws in this case the error:
UseBasesMask formatting error. A mask must be specified for each read. Number of reads: 3.
Indeed, according to RunInfo.xml there are 3 reads (with lengths 151, 8 (barcode), and 151 accordingly). If we specify three lengths in bcl2fastq call, e.g
… ---use-bases-mask Y*,I8,Y*
Then there is no error message and the program creates fastq files. Unfortunately they all are “Undetermined” (we obtain the same outputs if we don’t specify the –use-bases-mask parameter at all). That means imho that the bcl2fastq had problems with the extracting the barcode indices from the SampleSheet.csv data. We have edited the SampleSheet.csv according to the suggestion from the abovementioned guide: “ … [clear] the content in the “I5_index_ID” and “index2” columns”.