Count the numfer of reads supporting a pattern from a BAM file

0

Dear all,

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.


samtools

• 57 views



Source link