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