part0.2_mapping_to_genome.md

I usually use bowtie1 for mapping short 36-bp reads to human genome. bowtie2 is better for longer reads.

bowtie1:

bowtie -p 10 --best --chunkmbs 200 path/to/ref/genome -q my.fastq -S | samtools view -bS - > unsorted.bam

BWA-MEM is recommended for query sequences longer than ~70bp for a variety of error rates (or sequence divergence). Generally, BWA-MEM is more tolerant with errors given longer query sequences as the chance of missing all seeds is small. As is shown above, with non-default settings, BWA-MEM works with Oxford Nanopore reads with a sequencing error rate over 20%.

Use Teaser to test which mapper works the best for you.