secondary alignment and unique hit (NH:i:1)? tophat

[nachocab]

3000 of my single-end reads have the secondary alignment bit turned on (0x100) but they're reported as unique hits (NH:i:1). How is this possible?

I thought every read with a secondary alignment had to also have a primary alignment, but that's not what I get, for example, grep only returns one result for read WICMT-SOLEXA2_20A62AAXX:5:150:761:975

$ samtools view accepted_hits.bam | grep "WICMT-SOLEXA2_20A62AAXX:5:150:761:975"
WICMT-SOLEXA2_20A62AAXX:5:150:761:975	272	chr2	133038625	255	4M4I28M	*	0	0	AGACTGACCCATGTTCAACTGCTGTTCACATGGAAC	*	AS:i:-22	XN:i:0	XM:i:1XO:i:1	XG:i:4	NM:i:5	MD:Z:0G31	YT:Z:UU	NH:i:1
$

which has the NH:i:1 and the 0x100 (secondary alignment) and 0x10 (reverse strand) flags (0x100+0x10 = 272)

Any ideas?

[huyvuong]

Did you run tophat with --report-secondary-alignments on?

[nachocab]

I didn't, unless that's the default

[huyvuong]

the default is off, i.e "TopHat reports best or primary alignments based on alignment scores (AS)" (http://tophat.cbcb.umd.edu/manual.html)

[loard]

Might have been fixed in Tophat 2.0.2.