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Old 09-20-2016, 02:33 PM   #5
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Location: California

Join Date: Jul 2014
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Originally Posted by thermophile View Post
3. bcl2fastq or basespace is much much slower at demultiplexing. It used to take <30min to rerun a sample sheet, it's taking >4hours now.
Perhaps this is related to the number of cores you allow bcl2fastq to use?

Originally Posted by thermophile View Post
4. bcl2fastq doesn't allow you to set the indexing mismatch (at least tech support that I talked to didn't know how to globally set). It tries to allow 1 mismatch and only drops to exact match if the hamming distance is <3
from the bcl2fastq --help text:
  --barcode-mismatches arg (=1)
number of allowed mismatches per index
multiple entries, comma delimited entries, allowed; 
each entry is applied to the corresponding index;
last entry applies to all remaining indices
there is also this, which I have no idea what it does:
  --adapter-stringency arg (=0.9)                 adapter stringency
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