This is a description of the pipeline designed to analyze single 
nucleotide changes found in the mapped reads. The code should run 
on any Unix-like system supporting python 2.5 or better. The code 
is developed on MacOS X on python 2.5.

1. COMMAND LINE OPTIONS
2. BUILDING THE SNP DATABASE
3. RUNNING THE SNP PIPELINE


1. COMMAND LINE OPTIONS

To find out more about the settings for each script, type:

python $ERANGEPATH/<scriptname> 

to see the command line options. Note that all ERANGE command-line 
options are case-sensitive & that the scripts typically ignore 
command-line arguments that they do not recognize!


2. BUILDING THE SNP DATABASE

In order to check the candidate SNPs versus known SNPs, you will need 
to first download the corresponding dbSNP database file from UCSC and 
then build a sqlite version of it using:

python $ERANGEPATH/buildsnpdb.py ucscSNPfile outdb

e.g.

python buildsnpdb.py snp128.txt dbSNP128


3. RUNNING THE SNP PIPELINE

The runSNPAnalysis.sh shell script is designed to retrieve SNPs, filter
them against repeat annotations, cross-check them against known SNPs and
annotate the novel SNPs. It will automatically run a set of python scripts 
that are required for the SNPs analysis using the RDS (Read DataSet) file. 
This script assumes the existence of a known SNP database as described in 
the previous section as well as of a repeatmask database

Usage: $ERANGEPATH/runSNPAnalysis.sh genome rdsfile label rmaskdbfile dbsnpfile uniqStartMin totalRatio rpkmfile cachepages

where ERANGEPATH is the environmental variable set to the path to the directory holding the ERANGE scripts.

Parameters:
- genome: the name of the organism in the analysis.
- rdsfile: read DataSet file. See README.build-rds for 
more information.
- label: the file name of your choice for the analysis.
- rmaskdbfile: repeat mask database, a sqlite database file. See 
README.rna-seq for more information on creating the database.
- dbsnpfile: dbsnp database, a sqlite database file, built from the 
dbSNP database text file from UCSC. Please see command line option 
for building dbsnp sqlite database using buildsnpdb.py .
- uniqStartMin: the ratio of the number of unique reads supporting a 
SNP at base s and the maximum number of unique read coverage at base s .
5 is a good number to start with.
- totalRatio: the ratio of the number of reads supporting an 
expressed SNP at s and the total read coverage at s . 0.75 should allow 
you to get the homozygous SNPs.
- rpkmfile: rpkm file can be generated using the RNA-seq pipeline as 
described in README.rna-seq.  If you do not have that file, you can 
set it to NONE.
- cachepages: cache pages. Make sure to use as much caching as your 
system will accomodate. See README.build-rds for more information.

Example: $ERANGEPATH/runSNPAnalysis.sh mouse 24T4spike.rds 24Tspike rmask.db dbSNP128.db 5 0.75 c2c12rna.24R.final.rpkm 5000000 

version 3.0    January  2009 - logging
version 3.0rc1 December 2008 - major rewrite and speed-up of getSNPs.py and chksnp.py
version 3.0b2  December 2008 - bug fixes & ERANGEPATH variable