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