When will FASTQ files be N-masked in Local Run Manager, MiSeq Reporter, bcl2fastq, and BCL Convert?

A common step when creating FASTQ files is to trim adapter sequences. This removes sequencing artifacts that could negatively affect downstream analysis, such as mapping and alignment.

For libraries with short insert sizes (e.g. around 40bp or smaller), it's possible to observe entire reads of poly-N sequences. This is also referred to as N-masking. If the number of bases remaining after adapter trimming is less than --mask-short-adapter-reads value, the remaining sequences will be replaced with N-bases.

The following lists the Illumina software and the default --mask-short-adapter-reads used for analysis:

• Local Run Manager (LRM)

  • --minimum-trimmed-read-length 32

• MiSeq Reporter (MSR)

  • --minimum-trimmed-read-length 32

• bcl2fastq

  • --minimum-trimmed-read-length 22Note: bcl2fastq on BaseSpace (also referred to as Generate FASTQ) uses the default value of 35.

• BCL Convert

  • --minimum-trimmed-read-length 22

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