I need to find a short DNA sequence motif from a BAM file, because the wet biologist found a potential mutation from Sanger sequencing. I need to double check if this finding is also present in the RNA-Seq reads aligned to human hg19 reference genome (in a BAM). Is there any way to do this effectively?
I tried to use IGV and used the motif search (in Tools menu), but have no luck locating the sequenc (15 bp long). Any other approaches available?