bcl2fastq-V2 base mask issue for six and eight barcode length

Question

[BioRyder]

Hello ,

I have a Hiseq-4000 run data.Out of eight lane , 1,2,3,5,6,7,8 are eight index length and lane 4 is six lane index. I have made two sample sheet like sample sheet with 8 index barcode and sample sheet with 6 index. First I have demultiplexed the data (bcl2fast V2.16) with 8 index Sample sheet by using --use-bases-mask Y*,I8n,Y* base mask and got the out put .After wards I have tried to do demultiplex the data with 6 index length sample sheet by using --use-bases-mask Y*,I6n,Y* base mask. In Second case (6 base) got the following error

Error : One or more read masks do not match the number of cycles specified in RunInfo.xml, and a '*' was specified. There is no way to determine the number of cycles implied by the '*'. Base mask: y*'

Please can you tell me that how to use the base mask in such situation , same run with two type of index (6 and 8 length barcode).

Answer 1

[GenoMax]

Try --use-bases-mask Y*, I6n*,Y* for the second run with 6 bp index. Remember to specify a unique output location.

Manual for the latest bcl2fastq seems to indicate that it may be possible to do this via a single run by specifying the two bases mask this way

--use-bases-mask Y*, I8n,Y* --use-bases-mask 6:Y*, I6n*,Y*

This uses the second mask for lane 6 and the other mask for all other lanes.

[BioRyder]

Hello,

Y*,I6n*,Y* is worked for 6 bp Index. Thank you so much for your answer...