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.fa

Clipping Adapter: TCGTATGCCGTCTTCTGCTTG

Min. Length: 15

Non-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.fa

56918430

(divide this by 2 gives 28,459,215 reads)

wc -l s_8_sequence_clipped.fa

53161882

(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#0/1

GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGA

>ILLUMINA-08A740_0000:8:1:2219:1057#0/1

CAAGCGTCGGAGGTTTAGTCTTTCGTATGCCGTCTTCTGC

>ILLUMINA-08A740_0000:8:1:2316:1056#0/1

TACCTGGTTGATCCTGCCAGTAGTCGTATGCCGTCTTCTG

head -n 6 s_8_sequence_clipped.fa

>ILLUMINA-08A740_0000:8:1:2219:1057#0/1

CAAGCGTCGGAGGTTTAGTCTT

>ILLUMINA-08A740_0000:8:1:2316:1056#0/1

TACCTGGTTGATCCTGCCAGTAG

>ILLUMINA-08A740_0000:8:1:3041:1059#0/1

GAAGCTGCGGGTTCGAGCCCCGTCAGTCCCGCCA

Any ideas?

Thanks,

Ken