I aligned my RNA-seq against reference genome using tophat, I used the default aligner bowtie2.
And also the default parameters:
tophat -p 8 -G $annotation -o out $database L1_1.fq.gz L1_2.fq.gz
After got the results, I found out that in the unmapped.bam file, some reads have exact same sequences with the reference. The follow is one line in the unmapped.sam file:
DGZN8DQ1:360:H9RN8ADXX:1:1101:4791:1895 69 * 0 255 *
* 0 0 TTTTGCTTTCTGACTCTGTGCTTGTGCCTTCAAGACTTTCACAACGATTTTCTGCTCCTCAATAAGGAAAGCCCGAGATCGGAAGAGCACACGTCTGAAC CCCFFFFFHHHHHJJJJJJJIJJJHIJJJJJIJJJIJJJJIJJJJJIJJJJJJJJJJJJIJIJJJJJIJJJJJJHHFFDEDDDDDDDDDDDDDDDDDCCD
Does anyone know why the bowtie2 doesn't treat those reads as mapped? Thanks