Bcl2fastq read length

Question

[BioRyder]

Hi ,

I am using bcl2fastq 2.16.0 to convert BCL to fastq. Sequencing read length is 150. But I need reads with length120 (first 120 base) while converting bcl to fastq.So I have used base mask as --use-bases-mask Y120,I6n*,Y120. But I got the error "length is not matching with Runinfo.xml" (there read length is 150). Can any one suggest how to solve this .. ?

Answer 1

[Devon Ryan]

Try Y120n*,I6n*,Y120n* and see if that works.

BTW, why don't you just convert as normal and trim the resulting reads?

[h.mon]

Or you walk the "wise troglodyte" path, and edit RunInfo.xml. No, better not, just try Devon Ryan's suggestion.

[BioRyder]

Its worked well..Thanks Devon