adapter sequences fastx_toolkit zcat -f $input | fastx_clipper -l $minlength -a $clip_source.clip_sequence -d $keepdelta -o $output -v $KEEP_N $DISCARD_OPTIONS Minimum sequence length (after clipping, sequences shorter than this length will be discarded) Standard (select from the list below) Enter custom sequence enter non-zero value to keep the adapter sequence and x bases that follow it use this for hairpin barcoding. keep at 0 unless you know what you're doing. Yes No Output only clipped sequences (i.e. sequences which contained the adapter) Output only non-clipped sequences (i.e. sequences which did not contained the adapter) Output both clipped and non-clipped sequences **What it does** This tool clips adapters from the 3'-end of the sequences in a FASTA/FASTQ file. -------- **Clipping Illustration:** .. image:: ./static/fastx_icons/fastx_clipper_illustration.png **Clipping Example:** .. image:: ./static/fastx_icons/fastx_clipper_example.png **In the above example:** * Sequence no. 1 was discarded since it wasn't clipped (i.e. didn't contain the adapter sequence). (**Output** parameter). * Sequence no. 5 was discarded --- it's length (after clipping) was shorter than 15 nt (**Minimum Sequence Length** parameter).