First,I have built uscs.hg19.fasta index using bowtie2-build $mydir/ucsc.hg19.fastq ucsc.hg19.
and then,I use $dir/bowtie2 -c -k 3 -x $mydir/ucsc.hg19 -U TAGTGCT -S ex.sam,but i can't see the tag IH,why?Am I wrong or it is sth wrong with its code? I am just looking foward your reply.
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