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fastqSample
~~~~~~
::
usage: fastqSample [opts]
Input Specification
-I NAME input name (prefix) of the reads
-T T total number of mate pairs in the input (if not supplied, will be counted)
-L L length of a single read (if not supplied, will be determined)
-U reads are unmated, expected in *.u.fastq
Output Specification
-O NAME output name (prefix) of the reads (default is same as -I)
-A automatically include coverage or number of reads in the output name
-m L ignore reads shorter than L bases
-max don't sample randomly, pick the longest reads
Method 1: specify desired output coverage:
-g G genome size
-c C desired coverage in the output reads
Method 2: specify desired number of output pairs
-p N for mated reads, output 2N reads, or N pairs of reads
for unmated reads, output N reads
Method 3: specify a desired fraction of the input:
-f F output F * T pairs of reads (T as above in -t option)
0.0 < F <= 1.0
Method 4: specify a desired total length
-b B output reads/pairs until B bases is exceeded
Samples reads from paired Illumina reads NAME.1.fastq and NAME.2.fastq and outputs:
NAME.Cx.1.fastq and N.Cx.2.fastq (for coverage based sampling)
NAME.n=N.1.fastq and N.n=N.2.fastq (for coverage based sampling)
If -T is not supplied, the number of reads will be counted for you.
ERROR: no name supplied with -I.
ERROR: no method supplied with -c, -p, -f or -b
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