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Old 09-21-2016, 08:08 AM   #8
thermophile
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Location: CT

Join Date: Apr 2015
Posts: 243
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Quote:
Originally Posted by fanli View Post
Perhaps this is related to the number of cores you allow bcl2fastq to use?


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
Thanks! I'll have to see if i can change something in the sample sheet to set this
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Microbial ecologist, running a sequencing core. I have lots of strong opinions on how to survey communities, pretty sure some are even correct.
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