The load_fastq_directory function

The load_fastq_directory function is one of the main ways to get data _into_ NGLess. It takes the name of a directory

`bash $ find sample1 sample1/SRR8053346.pair.1.fq.gz sample1/SRR8053346.pair.2.fq.gz sample1/SRR8053346.single.fq.gz sample1/SRR8053355.pair.1.fq.bz2 sample1/SRR8053355.pair.2.fq.bz2 `

This will return a sample that contains _both paired-end and single-end data_:

  1. The paired-end dataset sample1/SRR8053346.pair.1.fq.gz - sample1/SRR8053346.pair.2.fq.gz
  2. The paired-end dataset sample1/SRR8053355.pair.1.fq.bz2 - sample1/SRR8053355.pair.2.fq.bz2
  3. The single-end dataset sample1/SRR8053346.single.fq.gz

Currently (as of version 1.4), NGLess supports the following

  • Extensions .gz and .bz2 are handled transparently
  • The extension (prior to the compression extension) must be either .fq or .fastq
  • Before the extension, one of .1/.2 or _1/_2 or _F/_R denotes the paired-end matching

If your data does not conform to these rules, we recommend that you use _symlinks_ to build a directory that does conform to it.

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