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Old 05-24-2017, 01:17 PM   #7
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Location: Maryland

Join Date: Dec 2016
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Originally Posted by GenoMax View Post
It is possible to get the index read as a separate fastq file with bcl2fastq v.2.xx. If you have access to the raw data folder you may want to check into getting that file. If those reads look like nothing you expect (to a large extent, there will always be permutations of bases that can't be explained easily but that fraction should be relatively small) then there must be an error in your experimental design (but you can worry about that later).
You can also tweak a file on the MiSeq to configure it to create index reads for every sample(and Undetermined) by following the guide here: It's basically just adding one line to a text file telling it to output index reads.
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