Get the positive and negative strands of reads in bam file for particular nucleotide position?
For example, If I have the bam file contains Chromosome:3 nucleotide_position:13226978, I want to find the no of reads mapped to particular nucleotide_position. It can be done by the pysamstats package using reads_all function.
Now, I want to find out positive and negative strands or reads to that particular nucleotide_position as well as gene-symbol associated with it?
How can I do this and can able extract relevant information?
I want to do it for list of bam files, so I am writing python script.
Any suggestions related to extracting strands as well as gene-symbol are really helpful to me. :)