Run Demultiplexing pipeline

There are 2 pipelines for demultiplexing; the first accepts BCL files as input, the second fastq files.

Demultiplexing from BCL files

Upload BCL files to the server according to the following instructions:

• Instructions for uploading data to the server

All original BCL file folders must be built according to Next-seq (or Hi-seq) machine requirements. Folder names should adhere to the template <date>_<machine name>_<run number>_<flowcell id>, e.g. “170802_NB501465_0140_AH3W3KBGX3”.

The pipeline converts bcl files to fastq files, and demultiplexes fastq files according to MAR-seq or True-seq (or semi- True-seq) protocols.

Demultiplexing from fastq files

The pipeline demultiplexes fastq files according to MAR-seq or True-seq (or semi- True-seq) protocols.

Upload fastq files to the server according to the following instructions:

• Instructions for uploading data to the server

Note that the pipeline get as input one file per read (i.e. one file for each of R1, R2, I1 etc.). Choose the root folder of the fastq files from the list.

If the sequencing is single read, choose the file with R1 in its file name for read 1, the file with either R2 or I1 for index read, and leave the read 2 field empty.

If the sequencing is paired end, choose the file with R1 in its file name for read 1, the file with R2 for read 2, and the file with I1 for index read. If no file name includes I1, choose one with R2 for index read, and one with R3 for read 2.