Filtering options

Filtering limits processing to regions or motifs of interest, reducing both runtime and output size.

1. Reference regions

When working with reference-to-signal alignments, bases are processed only if they fall within specified regions.

There are three ways to provide reference regions:

Flag	Description
--ref-regions <REF:START-END>	Specify regions directly (1-based, inclusive). Multiple regions space-separated.
--bed-file <PATH>	Provide regions from a BED file (0-based, start-inclusive, end-exclusive).
--positions-of-interest <REF:POS-HALFWINDOW>	Define positions with flanking windows. Coordinates are 1-based. See Positions with windows.

Positions with windows

This mode targets a specific site plus a window around it, e.g.: ChrA:8-4

1-based index:          1 2 3 4 5 6 7 8 9 0 1 2 3 4 5
Ref sequence:           A C G T A G C T A A A G T C T
Region of interest:          |--------X--------|

2. Motifs

Motif filtering works for both query- and reference-to-signal alignments. Only alignment segments exactly matching a provided motif are processed. (Requires fishnet align output level 2 or 3 to include sequence information.)

There are two ways to provide motifs:

Flag	Description
--motifs <MOTIF-1> ...	Provide motifs directly. Named automatically (motif1, motif2, …).
--motifs-file <FASTA>	Provide motifs via a FASTA file. Names are taken from the FASTA headers.

All motif matches within a read are processed.