This README file describes the contents of this ftp site

Contents
========

libraries/

*.Q0.filtered

Each of these files contains data for a Mouse ATLAS library.
The libraries have been filtered to remove tag sequences deemed to be
of low quality. Tags sequences have been clustered to remove tags likely
to be artifacts of highly abundant tag sequences.
Pooling all SAGE tags togather created the "meta-library"

The data in the files is in the following format (space seperated file):

<tag> - the SAGE tag
<tag count in library> - The number of times the tag is observed in the library
<tag p-value in library> - The library p-value of the tag
<tag count in metalibrary> - The number of times the tag is observed in the meta-library
<tag p-value in library> - The meta-library p-value of the tag

The file metaLibraryErrors.filtered contains data in the following format
<tag> - the SAGE tag
<tag count in metalibrary> - The number of times the tag is observed in the meta-library
<tag p-value in library> - The meta-library p-value of the tag

mappingFile:

The mapping file contains the location of all tags that map to a single location.
The mapping was performed against v32 of the mouse genome.
The file has the following format:
Major items are seperated by a "|"
Minor items are seperated by a " "

<tag info>|<location>|<location type>|<additional information>

<tag info> comprises
<tag> - the SAGE tag
the remaining fields are not used in this file

<location> comprises
<chromosome> - the chromosome that the tag is located on
<base pair> - the base pair that the tag sequence starts at (the base pair following the restriction site, "CATG")
<strand> - the strand that the tag is located on
the coordinates are on the mouse genome v32 and calculated using the ENSEMBL database

<location type> can be one of
EXONENSEMBL - Tag hits the coding region of an ensembl region 
UTRENSEMBL - Tag hits the UTR region of an ensembl gene
EXONNONENSEMBL - Tag hits an MGC or RefSeq transcript located at that position, but no ENSEMBL gene is found there
INTRON - None of the above and tag hits an intron of an ENSEMBL gene
GENOMIC - None of the above

<additional information>
provides further information on the genes in the vicinity of the tag
if the location type is EXONENSEMBL or UTRENSEMBL or INTRON, the next field provides the name of the ENSEMBL transcript (gene for INTRON)
if the location type is EXONENSEMBL or UTRENSEMBL, the remaining fields may indicate additional mgc, refseq and ensembl genes 
if the location type is EXONNONENSEMBL, mgc and refseq genes at this location will follow
if the location type is EXONENSEMBL or UTRENSEMBL or EXONNONENSEMBL, there may occasionally follow transcripts specified as "NOTLOCALIZED".
The hits to these transcripts could not be mapped back to genomic coordinates
if the location type is GENOMIC, there may follow another field specifying the CLOSEST GENE. "upstream" and "downstream" specify the position
of the tag relative to the gene. 


Please contact Asim Siddiqui <asims@bcgsc.ca> if you have any questions about this data.