Count the numfer of reads supporting a pattern from a BAM file
I have a
BAM file and I want to count how many reads have the following 4 patterns at chromosome region around 250bp:
AAAAAAAGAAAAA AAAAAAAGAAAAAA AAAAAAAAGAAAAAA AAAAAAAAGAAAAA
I have downloaded
ASCIIgenome software and tried something with
samtools mpileup. But I don't know how to do what I am looking for.
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