Tag Extraction #
Finding ’things’ in reads, and then using that information is called ’tagging'.
Extraction and downsteam steps are tied together with arbitrary ’labels'.
This allows you to efficiently perform multiple actions with one search, for example trim adapter tags and keep only reads that contain the adapter.
You first use one of the following steps to extract read information:
- Extract Anchor
- Extract Iupac
- Extract Length
- Extract Regex
- Extract Region
- Extract Regions
- Extract Regions of Low Quality
- Remove Tag
- Store Tag in Comment
- Store Tag in Sequence
- Store Tag Location in Comment
- Tag Other File by Name
- Tag Other File by Sequence
- Store Tag in Fast Q
- Extract Gccontent
- Extract Iupacsuffix
- Extract Low Complexity
- Extract Low Quality End
- Extract Low Quality Start
- Extract Mean Quality
- Extract Ncount
- Extract Poly Tail
- Extract Qualified Bases
- Hamming Correct
- Tag Duplicates
- Extract Iupac
And then you get to use one of the following to make use of it :
- TrimTag to trim the read at the tag
- LowercaseTag to trim the read at the tag
- AddTagSequenceToName to add the tag sequence to the read name.
- FilterTag to keep or remove reads matching the tag