ExtractRegion #

Extract a fixed position region.

[[step]]
    action = "ExtractRegion"
    start = 5
    length = 8
    source = "read1" # Any of your input segments, name:<segment_name> or tag:<any_location_or_string_tag>
    anchor = "Start" # 'Start' or 'End' - start is relative to this
    out_label = "umi"

This transformation extracts a fixed-length region from the specified read at a given position and stores it as a tag.

Start positions (anchor = start) are 0-based.

End positions require negative starts (as in python, start=-1, length=1 is the last character).

Use ExtractRegions if your region is actually multiple regions (possibly from different segments).

If the read is shorter than requested, the region will be shorter (and might be of varying length).

The anchor is necessary since the source must not necessarily be a read, but can also be a previously found tag (e.g find an adapter, then take 6 bp after it).

For multi-region spanning tags as sources, regions outside the original tag will be outside the leftmost/rightmost position.

I must still fall within the read though, or it will yield a ‘missing’ region.