The gto_fastq_split splits Paired End files according to the direction of the strand ('/1' or '/2'). It writes by default singleton reads as forward stands.
For help type:
./gto_fastq_split -h
In the following subsections, we explain the input and output paramters.
The gto_fastq_split program needs a stream for the computation, namely the input standard. The input stream is a FASTQ file.
The attribution is given according to:
Usage: ./gto_fastq_split [options] [[--] args]
or: ./gto_fastq_split [options]
It writes by default singleton reads as forward stands.
-h, --help show this help message and exit
Basic options
-f, --forward= Output forward file
-r, --reverse= Output reverse file
< input.fastq Input FASTQ file format (stdin)
> output Output read information (stdout)
Example: ./gto_fastq_split -f -r < input.fastq > output
Output example :
Total reads : value
Singleton reads : value
Forward reads : value
Reverse reads : value
An example of such an input file is:
@SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=72 1
GNNTGATGGCCGCTGCCGATGGCGNANAATCCCACCAANATACCCTTAACAACTTAAGGGTTNTCAAATAGA
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IG9ICIIIIIIIIIIIIIIIIIIIIDIIIIIII>IIIIII/
@SRR001666.2 071112_SLXA-EAS1_s_7:5:1:801:338 length=72 2
NTTCAGGGATACGACGNTTGTATTTTAAGAATCTGNAGCAGAAGTCGATGATAATACGCGNCGTTTTATCAN
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII6IBIIIIIIIIIIIIIIIIIIIIIIIGII>IIIII-I)8I
The output of the gto_fastq_split program is a set of information related to the file read.
Using the input above, an output example for this is the following:
Total reads : 2
Singleton reads : 0
Forward reads : 65536
Reverse reads : 1
Also, this program generates two FASTQ files, with the reverse and forward reads.
An example of the forward reads, for the input, is:
@SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=72 1
GNNTGATGGCCGCTGCCGATGGCGNANAATCCCACCAANATACCCTTAACAACTTAAGGGTTNTCAAATAGA
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IG9ICIIIIIIIIIIIIIIIIIIIIDIIIIIII>IIIIII/