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

Join Date: Jul 2014
Posts: 198
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Quote:
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?

Quote:
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:
Code:
  --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:
Code:
  --adapter-stringency arg (=0.9)                 adapter stringency
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