http://bowtie-bio.sourceforge.net/tutorial.shtml

soft add +bio-align-rna

1) performing alignment

bowtie e_coli reads/e_coli_1000.fq

bowtie -t indexes/e_coli reads/e_coli_1000.fq e_coli.map
-t: timing statistics
pre-bult E. coli index included with Bowtie is built from the sequence for strain 536, known to cause urinary tract infections


2) Building a new index:
bowtie-build genomes/NC_008253.fna e_coli_new
 These files constitute the index. Move these files to the indexes subdirectory to install it. 

test the newly built index
bowtie e_coli_new reads/e_coli_1000.fq

3)Finding variations with SAMtools:

bowtie -S e_coli reads/e_coli_10000snp.fq ec_snp.sam 

samtools view -bS -o ec_snp.bam ec_snp.sam

samtools sort ec_snp.bam ec_snp.sorted 

samtools pileup -cv -f genomes/NC_008253.fna ec_snp.sorted.bam
---pileup command should print records for 10 distinct SNPs, the first being at position 541 in the reference. 


