mkfastq scATAC 10X genomics — index read issue

2 hours ago by

Hello,
I am analyzing scATAC-seq that was performed using 10X genomics v1.1. For sequencing, the index (i7) read is supposed to be 8bp, but when the libraries were sequenced, the i7 read was 16bp. Therefore, when I run cell ranger-atac mkfastq, I receive an error that the length of the index read does not match the length of the specified indices for the samples. Is there a way to use --use-bases-mask option to correct this issue so I can properly demultiplex samples? The library was sequenced on a NextSeq 500.

Thanks!
Brian