Quote:
Originally Posted by samd
Hi all,
appreciate the responses
@nucacidhunter
1. Primers are the EMP 515-806 V4 region
2. Cluster density was about 477 if I remember correctly
3. Just 1 library. Usually I was doing 160 samples per run and this time I reduced the run to about 100 samples and still got crummy results
4. Read output was actually 25M and then 23M PF which I guess is great actually but then 40% were undetermined and then when I import the fastq files into QIIME2 I only get about 7 million reads (this is before dada2, so still the entire files).
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Run stats seems within specs for the library type although they seem to be more cautious. To increase output safely following can be done:
1- Increasing cluster density to around 800k/mm2
2- Tunning PhiX% to 20 if after mapping undetermind reads majority of them origoinats from PhiX. Undetermind reads also could be reads that their index has not been assigned as a result of miss-matches in custom index primer or PCR primers itself.