→ Install Bowtie2 Examplemapping short reads against E. coli 2011 outbreak genome# Create bowtie2 index database # example genome: German 2011 E.coli outbreak (database name: ecoli) bowtie2-build GCF_000299455.fna ecoli # Bowtie2 mapping
# map reads (sample.fastq) against the E. coli genome database 'ecoli'
bowtie2 -x ecoli -1 SAMPLE_r1.fastq -2 SAMPLE_r2.fastq -U SAMPLE_single_reads.fastq --no-unal -p 12 -S SAMPLE.sam -1 read 1 of paired reads -2 read 2 of paired reads
-U single unpaired reads -S SAMPLE.sam write bowtie2 output in SAM format to file SAMPLE.sam --no-unal ignore reads that failed to align -p 12 use up to 12 parallel processors → SAMtools to filter and convert result of SAMPLE.sam
→ Tablet-viewer to graphically view the mapped read alignment
read more http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml |
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