am trying to use different softwares for my new sequencing protocol and am comparing 3 different alignment tools:
Now am on the step in which i want to retrieve unique mapped reads and as in the community has been already explained different alignment tools have different solution. For example:
- BWA uniquely mapped reads are retrieved selecting Quality Score > 0 and removing unmapped reads;
- Bowtie2 uniquely mapped reads are retrieved removing all the reads with MAPQ < 1 as well as removing the unmapped reads and not primary aligned
For Segemehl i can't use these information since in the SAM format are not present the flags in wihich i can retrieve these information but i can align using the parameter multiple hits (-M). So can I use this parameter -M to 1 in order to extract unique mapped reads? Does Multiple Hits means that the reads are aligned in several regions of the Genome, so that -M > 2 means that the reads are mapped in different regions of the genome and then are not uniquely mapped?
Thanks in advance for any suggestions.