The Frontline Support team will be offline February 18 for President's Day but will be back February 19th. Thank you for your patience as we get to all of your questions!
Dear GATK team,
I am doing an allele-specific expression analysis using RNA-seq data. I am trying to run ASEReadCounter to calculate read counts per allele and use Mamba (or other downstream tool) for the allele-specific expression analysis.
My question is: which bam file I should have as an input for the ASEReadCounter do you recommend. Is the bamout file generated by HaplotypeCaller that was after local assembly and re-alignment better? or should I just input the pre-processed and aligned RNA-seq?
Thank you in advance for your help.