Hi, 
I'm using the fastx_toolkit (v0.0.13) command line scripts. 
When using fastx_clipper, I get: 
fastx_clipper -a TCGTATGCCGTCTTCTGCTTG -v -c -l 15 -M 5 -i s_8_sequence.fa -o 
s_8_sequence_clipped.faClipping Adapter: TCGTATGCCGTCTTCTGCTTGMin. Length: 
15Non-Clipped reads - discarded.Input: 227673720 reads.Output: 212647528 
reads.discarded 3527200 too-short reads.discarded 725608 adapter-only 
reads.discarded 10773384 non-clipped reads.discarded 0 N reads.
The s_8_sequence.fa file is 2.2Gb, s_8_sequence_clipped.fa file is 1.7Gb.... 
seems like fastx_clipper is reporting way too many reads in this instance.  I 
also tried without the -M option but same thing. 
I checked with:
wc -l s_8_sequence.fa56918430(divide this by 2 gives 28,459,215 reads)
wc -l s_8_sequence_clipped.fa53161882(divided by 2 gives 26,580,941 reads)

There has never been such a discrepancy with this tool. 
I'm not sure if I'm doing something silly this time round, or somethings 
changed in my system that's affecting fastx_clipper counting. 
Heres a couple of lines from input and output:
head -n 6 
s_8_sequence.fa>ILLUMINA-08A740_0000:8:1:1736:1055#0/1GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGA>ILLUMINA-08A740_0000:8:1:2219:1057#0/1CAAGCGTCGGAGGTTTAGTCTTTCGTATGCCGTCTTCTGC>ILLUMINA-08A740_0000:8:1:2316:1056#0/1TACCTGGTTGATCCTGCCAGTAGTCGTATGCCGTCTTCTG
head -n 6 
s_8_sequence_clipped.fa>ILLUMINA-08A740_0000:8:1:2219:1057#0/1CAAGCGTCGGAGGTTTAGTCTT>ILLUMINA-08A740_0000:8:1:2316:1056#0/1TACCTGGTTGATCCTGCCAGTAG>ILLUMINA-08A740_0000:8:1:3041:1059#0/1GAAGCTGCGGGTTCGAGCCCCGTCAGTCCCGCCA

Any ideas? 
Thanks, 
Ken                                       
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