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Here are two examples for mapping 100,000 synthetic BS reads with base calling errors onto reference genome.


Example 1: The BS reads are simulated as they were generated by the Cokus et al.'s library protocol-- most of reads have tags.

Example 2: The BS reads are simulated as they were generated by the Lister et al.'s library protocol-- ALL reads do not have tags.


Two folders are placed at ./tag and ./notag.

Each folder includes BS_Seeker and the synthetic BS reads. The reference genome “chr1.fa” can be found at ./ .


Example 1. MAPPING READS WITH TAGS


BS reads filename:BS_reads_100k_tag.txt (100,000 BS reads of 36 bp, 5 (tag)+31 (sequence))

Reference genome filename: chr1.fa


Place BS Seeker, BS reads file, and the reference genome file in the same folder.


Preprocessing reference genome:

In command line type (under ./tag/):

python Preprocessing_genome.py --f chr1.fa --t Y --p ~/bowtie-0.10.0/  > log_Preprocessing_genome.txt



This will build up a folder of Bowtie reference libraries at ./reference_genome/


Mapping and post-processing:

In command line type (under ./tag/):

python BS_Seeker.py --i BS_reads_100k_tag.txt -t Y -f TCTGT -r TCCAT -e 36 -p ~/bowtie-0.10.0/ -d ./reference_genome/ -m 2 -o myoutput.txt



This will produce an output of unique alignments, and a log file.


In this example, 90542 (90.5%) BS reads are uniquely mapped.


Example 2. MAPPING READS WITH NO TAGS


BS reads filename:BS_reads_100k_notag.txt

Reference genome filename: chr1.fa


Place BS Seeker, BS reads file, and the reference genome file in the same folder.


Preprocessing reference genome:

In command line type (under ./notag/):

python Preprocessing_genome.py --f chr1.fa -t N  --p ~/bowtie-0.10.0/  > log_Preprocessing_genome.txt



This will build up a folder of Bowtie reference library at ./notag/reference_genome/


Mapping and post-processing:

In command line type (under ./notag/):

python BS_Seeker.py --i BS_reads_100k_notag.txt -t N -e 36 -p ~/bowtie-0.10.0/ -d ./reference_genome/ -m 2 -o myoutput.txt



This will produce an output of unique alignments, and a log file.


In this example, 91390 (91.4%) BS reads are uniquely mapped.