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Demultiplexer manual
Updated Jan 9, 2015 by joel.sjo...@gmail.com

Introduction

The most up-to-date version of the demultplexer is written in Python, although an older more specialized C++ version is also included in the multiplexer folder. The info beneath refers to the Python version.


Input

The input to the demultiplexer consists of two files:

  1. The file with the true barcodes ("IDs").
  2. The file with the read sequences, either as a FASTQ file or as a SAM file.

The true barcodes file should be tab-delimited, with the true barcodes appearing in column 1, and arbitrary information appearing in columns 2,...:

AACCGGTT   11   44   Some attribute
CCAATTGG   33   22   Another attribute
TTCCGGAA   22   99   Yet another attribute
...

Output

The output from the demultiplexer consists of (at most) 4 files:

  1. A tab delimited file containing the annotation of each read, and the demultiplexing result, output.result.txt.
  2. A FASTQ/SAM file (same as the input format) containing the perfectly or unambiguously mapped reads, augmented with information for the barcode and attributes, output.mapped.fastq/sam. This information appears in the description field in FASTQ (on the same line as the annotation), and in their own fields in SAM format.
  3. A FASTQ/SAM file, as above, but for the ambiguously mapped reads, output.ambiguous.fastq/sam. Each read will appear multiple times, but with different barcodes and attributes added. The order of the ambiguous hits will be randomized.
  4. A FASTQ/SAM file, as above, but with unmapped reads, output.unmapped.fastq/sam.

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