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Old 05-07-2016, 06:18 AM   #3
wendy_H
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Location: dallas

Join Date: May 2016
Posts: 5
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It's number 1. The most recent MiSeq was run using 2x300bp, in about 20% of the sequencing output, I get about 60bp read length followed by low quality nucleotides, which I think indicate number 1 happening.

For read length calculation, I ran the enriched library on DNA gel so I could get an estimate of average fragment length. I should correct myself, the cluster density (~1100K/mm2) and pass filter rate (~90%) for the MiSeq run was great. The problem I had was distribution of % reads. For some of my samples, they were sequenced for only 0.2% to 1% among all sequencing samples; for some other samples, they were sequenced 24%. Theoretically if I have 18 samples and I loaded them equally, I am expecting about 5.5% for each get sequenced.
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