I am new in NGS analysis. In my study, I sequenced sample with 5 of sperm cells on the Miseq Illumina platform. After mapping using Bowtie2 on Galaxy webpage and got BAM file. And I need to solve two things:
- How to determine how many sperm cells in one sample (is it 5 of sperm cells?)
- Calculate the ratio of X and Y chromosome sperm cells.
Currently, I do not know which tools or how can deal with these issues (mentioned above). could you help out?