Hello, I used "Map with Bowtie for Illumina" tool to map the sequences reads to the reference genome and didn't change any settings (commonly used). Just wondering does the mapping results contain unmapped reads? After the work done, it showed "Map with Bowtie for Illumina on data 59 and data 5: mapped reads". Because it has "mapped reads" in there, I was guessing the unmapped reads already been removed. Am I correct?
Thank you very much, Ren