How to avoid Ns in small RNA or short reads when running BCL Convert

Small RNA reads, and reads from other applications where inserts are shorter, are sometimes masked with Ns after FASTQ generation, resulting in the reads being 35 Ns instead of the actual basecalls. N-masking occurs when the length of a read is below the default minimum trimmed read length of the software (35) and the adapter masking length (22) after adapter trimming.

To avoid N-masking when using BCL Convert, add the following two settings in the [BCLConvert_Settings] section of a v2 sample sheet:

MinimumTrimmedReadLength,5 MaskShortReads,5

The application of these settings can be used with standalone BCL Convert as well as with BCL Convert in BaseSpace and/or Illumina Connected Analytics (ICA).

For any feedback or questions regarding this article (Illumina Knowledge Article #9157), contact Illumina Technical Support [e-mail].