I am using sickle (https://github.com/najoshi/sickle) for trimming my 5'ends and 3'ends to give me good quality reads from my Miseq raw data. The description of the software says that there is possibilities to disable 5'ends and remove all the reads with Ns in it. And this could be done using -n command.
I am using pair end reads and unfortunately I am unable to use the -n command as the options described on GitHub.
My command is
$ sickle pe -f input_file1.fastq -r input_file2.fastq -t sanger -o output_file1.fastq -p output_file2.fastq -s single_N_trimmed.fastq -n
The error message shown here is
invalid option --n
the options shown on my terminal when sickle pe --help is typed are
Options: -f, --pe-file1, Input paired-end fastq file 1 (required, must have same number of records as pe2)
-r, --pe-file2, Input paired-end fastq file 2 (required, must have same number of records as pe1)
-t, --qual-type, Type of quality values (illumina, phred, sanger) (required)
-o, --output-pe1, Output trimmed fastq file 1 (required)
-p, --output-pe2, Output trimmed fastq file 2 (required)
-s, --output-single, Output trimmed singles fastq file (required)
-q, --qual-threshold, Threshold for trimming based on average quality in a window. Default 20.
-l, --length-threshold, Threshold to keep a read based on length after trimming. Default 20.
--help, display this help and exit
--version, output version information and exit