low Q30 in index, miseq v3 600
I recently ran a v3 600 cycle kit on a Miseq and the Q30 values dropped way down in the index read. The sample was 2-plex using N701 and N702. The basecalls in the index fastq look like junk. Any ideas as to what the problem could be? I'm using the standard primers.
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You are using one of the recommended tag combinations for 2-plex libraries so that part should be ok. So you were not able to demultiplex the data (are there lots of N's in tag reads? Have you talked with tech support? -
One possible issue would be design or oligo manufacturing fault if you have not used actual Illumina Nextera kit for library prep which seems to be the case. I wonder what was the %reads identified.Comment
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I had the same issue, but in my case custom sequencing primers were used. Tech support suggested the issue is coming from the primers, but previous runs were just fine. My % reads identified was 11 %. Pretty low. Any thoughts?Comment
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