Unexpected observations after mapping LongSAGE tags to the human genome.

ABSTRACT:

Background

SAGE has been used widely to study the expression of known transcripts, but much less to annotate new transcribed regions. LongSAGE produces tags that are sufficiently long to be reliably mapped to a whole-genome sequence. Here we used this property to study the position of human LongSAGE tags obtained from all public libraries. We focused mainly on tags that do not map to known transcripts.

Results

Using a published error rate in SAGE libraries, we first removed the tags likely to result from sequencing errors. We then observed that an unexpectedly large number of the remaining tags still did not match the genome sequence. Some of these correspond to parts of human mRNAs, such as polyA tails, junctions between two exons and polymorphic regions of transcripts. Ano

SUBMITTER: Keime C 

PROVIDER: S-EPMC1884178 | biostudies-literature | 2007 May

REPOSITORIES: biostudies-literature