Samples that pass QC are finally ready to be mapped and analyzed. The researches will be consulted on what genome version they would like to map to, although the default would be to use the latest version available. On special request, we can try to use an older genome or even a custom one.
Reads are mapped using software that is pertinent to the type of experiment being done. Usually, we use Bowtie2 for single-end sequencing and BWA for paired-end sequencing, although using other software is not out of the question.
Duplicates are removed from the mapped data using PICARD and reads with quality less than 10 are also filtered out. This leaves us with an alignment file with analysis-ready data.