The gto_fastq_minimum_read_size filters the FASTQ reads with the length smaller than the value defined.
For help type:
./gto_fastq_minimum_read_size -h
In the following subsections, we explain the input and output paramters.
The gto_fastq_minimum_read_size program needs two streams for the computation, namely the input and output standard. The input stream is a FASTQ file.
The attribution is given according to:
Usage: ./gto_fastq_minimum_read_size [options] [[--] args]
or: ./gto_fastq_minimum_read_size [options]
It filters the FASTQ reads with the length smaller than the value defined.
If present, it will erase the second header (after +).
-h, --help show this help message and exit
Basic options
-s, --size= The minimum read length
< input.fastq Input FASTQ file format (stdin)
> output.fastq Output FASTQ file format (stdout)
Example: ./gto_fastq_minimum_read_size -s < input.fastq > output.fastq
Console output example:
Total reads : value
Filtered reads : value
An example of such an input file is:
@SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=60
GGGTGATGGCCGCTGCCGATGGCGTCAAATCCCACCAAGTTACCCTTAACAACTTAAGGG
+SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=60
IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IG9ICIIIIIIIIIIIIIIIIIIIIDIII
@SRR001666.2 071112_SLXA-EAS1_s_7:5:1:801:338 length=72
GTTCAGGGATACGACGTTTGTATTTTAAGAATCTGAAGCAGAAGTCGATGATAATACGCGTCGTTTTATCAT
+SRR001666.2 071112_SLXA-EAS1_s_7:5:1:801:338 length=72
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII6IBIIIIIIIIIIIIIIIIIIIIIIIGII>IIIII-I)8I
The output of the gto_fastq_minimum_read_size program is a set of all the filtered FASTQ reads, followed by the execution report.
The execution report only appears in the console.
Using the input above with the size values as 65, an output example for this is the following:
@SRR001666.2 071112_SLXA-EAS1_s_7:5:1:801:338 length=72
GTTCAGGGATACGACGTTTGTATTTTAAGAATCTGAAGCAGAAGTCGATGATAATACGCGTCGTTTTATCAT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII6IBIIIIIIIIIIIIIIIIIIIIIIIGII>IIIII-I)8I
Total reads : 2
Filtered reads : 1