the question about fastx_clipper
i want to compare the result of fastx_clipper with my R coding
the query.fastq file include 25000 entries of data,
1. fastx_clipper -a AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTGAAACAAA -l 0 -i
query.fastq -o fastx_output -Q33
output 24334 entries
2. fastx_clipper -a AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTGAAACAAA -c -l 0 -i
query.fastq -o fastx_output -Q33
output 2974 entries
3. fastx_clipper -a AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTGAAACAAA -C -l 0 -i
query.fastq -o fastx_output -Q33
output 21360 entries
4. fastx_clipper -a AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTGAAACAAA -k -l 0 -i
query.fastq -o fastx_output -Q33
output 364 entries

so 2+3=１, but 2+3+4 Not=25000
so I compared 25000-24334= 666 with 4, found 302 not in 4
when i run the same parameter with 4 on those 666 entries, i can only output
12 entries

when i trimmed the same adaptor on 666 entries, the output is only 12
entries.

who can tell me why?

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