I have separated the reads aligned in the positive and negative strand of the genome from the sam files of my experiments. Now i need to play with the fasta sequences of the reads mapped. I have to select the first n nucleotides that were soft clipped. To do this i have to consider the number of nucleotides soft clipped from the corresponding fasta sequence in the sam file. This I have to do for the positive and negative strand.
Now my question is:
for the reads aligned in the negative strand, should i have to consider the last nucleotides as soft clipped from the fasta sequence that is in the sam file? Or the reads have been already converted by the tool that am using?
Am using bowtie2 to align the reads and i cannot find in the tutorial of the tool this information.
If someone can help this would be really appreciated! Thanks in advance.