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Hi guys, I'm new to analyzing RNA-seq data. I'm looking to compare mutation rates between two different populations.
Right now, I've used bowtie2 to align to hg19. I'm not entirely sure where to go next (if there's a tool within bowtie2 or if I should be using something else). I know I have the alignment rate, but I'd like to have an assessment of discrepancy with the reference (insertions, deletions, substitutions, etc). Are there any easy tools to give a global assessment like that? Otherwise, I was planning on just parsing the alignment SAM output with MATLAB.
Any advice would be much appreciated. Thanks!
Right now, I've used bowtie2 to align to hg19. I'm not entirely sure where to go next (if there's a tool within bowtie2 or if I should be using something else). I know I have the alignment rate, but I'd like to have an assessment of discrepancy with the reference (insertions, deletions, substitutions, etc). Are there any easy tools to give a global assessment like that? Otherwise, I was planning on just parsing the alignment SAM output with MATLAB.
Any advice would be much appreciated. Thanks!