Hi all,
I have a SAM file produced by TopHat 2 (version 2.0.8) in which I find these two following mates that I can't explain:
HISEQ4_0101:8:1101:10030:81268#TGACCA 73 17 22696364 50 67M * 0 0 ATGGATATGAATTTTTTGCTAAACGACAATTGGTAACCCTATTTTCAGCCCCAAATTACTGTGGCGA CC@FFFFFHHHHHJJIJJJJJJJJIDGEIEIJDBDGICHCGIJJIJIJIJJIHJJIGHIEIHEFCD? MD:Z:67 RG:Z:1 XG:i:0 NH:i:1 NM:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:A:+ YT:Z:UU
HISEQ4_0101:8:1101:10030:81268#TGACCA 153 17 22696364 50 101M * 0 0 ATGGATATGAATTTTTTGCTAAACGACAATTGGTAACCCTATTTTCAGCCCCAAATTACTGTGGCGAGTTTGATAATGCTGGTGGAATGATGAGTGTGGAT DDEDDEEDDDBDBDDDDDDDDDDDEEEFFEFFFHE?FIHGGGHGJJIJJIIHIJGHDBJJJIGHHHCIIIIIJIJIIIJJJIJJJJJIHHGHGFFFFDBB< MD:Z:101 RG:Z:1 XG:i:0 NH:i:1 NM:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:A:+ YT:Z:UU
Why is there a star in the 7th field instead of an equal as expected ?
Cheers
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mathieu.bahin
there is a big problem with tophat2:
And I'm still waiting for an answer...
Did you ever try feeding a few of those reads (only non-spliced ones) into bowtie2 while playing with the --dovetail option? I suspect that it's bowtie2 that's actually the issue here.
I tried to align the two reads with bowtie2 only (+default opts). The SAM flags were OK.
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You might check what settings tophat2 is using when it's running bowtie2. That might be considered a "dovetail" mapping in bowtie2, so it wouldn't be valid for mates by default (try feeding that to bowtie2 by itself while playing with the settings to check this).