Genome Sciences Center - SAGE Summary HELP PAGE

C. elegans SAGE Summary Help

This help page outlines the options available for applying SAGE tag sequence quality filtering and tag-to-gene mapping to the available C. elegans SAGE libraries. There are two SAGE protocols, short SAGE (tag length is 14) and LongSAGE (tag length is 21). Please be advised that we only display 10mers for short SAGE and 17mers for LongSAGE, since all tags contain the same NlaIII anchoring enzyme recognition site (CATG).

Tag Filtering Criteria

Search Options

Tag-Mapping Options

Tag Filtering Criteria

Library

A library refers to the collection of SAGE tags derived from a particular transcription profiling experiment. The libraries below have been derived from worms in various life stages or tissues.

ID	Type	Description
SWL12	short	N2 L1 Larvae
SWL21	short	N2 L2 Larvae
SWL32	short	N2 L3 Larvae
SWL41	short	N2 L4 Larvae
SWN21	short	N2 embryos
SWAG1	short	glp-4 micro-dissected gut
SWAG2	short	glp-4 adult
SWYA1	short	N2 young adult
DAUER	short	dauer (Jones et al. 2001)
DAU_q2	short	dauer with quality
MIXED	short	mixed stage (Jones et al. 2001)
MIXq2	short	mixed stage with quality
SWEM1	long	FACS sorted embryonic muscle cells
SWEG1	long	FACS sorted embryonic gut cells
SWN22	long	N2 embryos

Tag count sorting order

The final set of tags which have been processed through by quality filtering and tag-to-gene mapping can be displayed in order of ascending or descending tag count in the library.

Overall Sequence Quality

There is a sequence quality score associated with each SAGE tag sequence. If no quality score is associated with a tag, no quality filtering will be applied. Scores can be interpreted as follows:

0.99 = cumulative phred score of 20
0.999 = cumulative phred score of 30
0.9999 = cumulative phred score of 40

Only those tags with a quality score at or above the indicated level will be retained for further filtering and mapping.

Small Family Sequence Quality

Small family SAGE tag refers to those tags with a count of 2 or 3. At least one of the tags must have a score at or above the indicated level for these low abundance tags to be retained for further analysis. This quality filter serves to remove tags that have may have been derived from sequencing errors.

Singleton Sequence Quality

A singleton is a SAGE tag with only 1 occurrence in the corresponding library. Rare tags are likely to be derived from sequencing error or PCR mis-incorporation, so applying a higher quality filter may be appropriate for singletons or rare (small family) tags.

Minimum tag count to show

View only those SAGE tags with a count higher or equal to the set value. Processing time will be decreased by selecting a higher number, as most SAGE tags are of low abundance.

Remove duplicate ditags

Duplicate ditags are artifacts generated during the SAGE procedure. Typically, tags derived from duplicate ditags are removed from the library.

Show unmatched tags

An attempt is made to map each SAGE tag to its corresponding gene or another specified source (see Tag-Mapping Options). Checking this box displays tags that do not map to any of the specified sources (e.g. Coding RNA, Mitochondria), in addition to the tags that do map to genes. To see only tags which do not map to the specified sources, see "Show only unmatched tags".

Resolve ambiguity to lowest position match

SAGE tag-to-gene mapping finds the gene from which a SAGE tag was derived, and the tag's location within the corresponding gene. Each CATG in a sequence is considered a possible NlaIII cut site and therefore marks the location of a potential tag. The 3' most CATG site is referred to as position 1, and the next 3' most CATG site is referred to as position 2, etc.

Quite often, a given SAGE tag will map to multiple genes (non alternative splice variants). They may also map to different tag positions in different genes. Unchecking this box will result in the display all of all possible tag-to-gene mappings. Since SAGE tags are most likely to be derived from a position 1 NlaIII site, the ambiguity of some of these mappings can be resolved by choosing the mapping that places the tag in the lowest position within a gene. Only these mappings will be displayed in the output if this box is checked.

This option applies to Coding RNA only.

Show only unmatched tags

Check this box to view only unmatched tags (i.e. tags that do not map to any of the specified sources).

Show only unambiguous tags

Some SAGE tags map to only one gene (unambiguous tags), others map to multiple genes (ambiguous tags). Check this box to view unambiguously mapped tags only. Unambiguously mapped tags are first identified by resolving tag-to-gene mappings to the lowest position match (see above). Those mappings that can be resolved are considered unambiguous. Those that cannot be resolved (e.g. a tag maps to position 1 in 2 different genes) are considered ambiguous.

This option applies to Coding RNA, Other RNA and Mitochondrial only.

Hide antisense tags

Antisense tags refer to those tags that map to the antisense strand of a coding sequence. Checking this box will allow you to hide antisense tag mappings.

This option applies to Coding RNA only.

Output raw text only

The default format for output is HTML. This option allows users to output the results in plain text format, with one record per line. This option is intended for exporting machine-readable output for downstream processing.

Search Options

Show items with the keyword

This option displays only the tags containing the keyword in their associated mapping/gene description information.

Hide items with the keyword

This option will allow users to hide the tags with mapping/gene description information containing the keyword.
If both 'Show items with the keyword' and 'Hide items with the keyword' terms are present, and if the tag information contains both of these terms, "Hide term" will override "Show term" and the tag not be displayed.

Tag-Mapping Options

Coding RNA

SAGE tags will be mapped to protein-coding sequences derived from a conceptual C. elegans transcriptome, with gene models based on a recent WormBase release (e.g. version WS110). The version of the WormBase release is indicated on the SAGE Summary front page.