We are using an Illumina MiSeq machine. Sample sheet generation using Illumina’s software is a lot of work so we just made our own layout in excel which finished sample sheet is the same as Illumina’s (in csv format). It just so happened that in our latest run the header of index i7 which is supposed to be “index” was changed to “index1”. And this caused the bcl files not to be demultiplexed to fastqs. Also, there is no read for this index in the MiSeq output-- there only 3 reads wherein there should be 4 reads. Is there still a way to demultiplex it on the MiSeq Control Software, like editing the sample sheet or the runinfo.xml file?