Hello all,

I have seen a weird problem with the TopHat2 output with an accepted.bam file.

Some query name are missing like following:

    73    chr10    27314766    50    75M    *    0    0    NTTCTGTTTCACTTCTCATAAACCATATTCTCAACCACACACTCATAAACCATTACTTGGTGCAGATTCCTTTTG    #AAFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJFJFFFJAFJJJJJJJAJAFA7FAFF    AS:i:-1    XN:i:0    XM:i:1    XO:i:0    XG:i:0    NM:i:1    MD:Z:0C74    YT:Z:UU    NH:i:1    XS:A:-
    89    chr12    69096534    50    31M6453N44M    *    0    0    ATTAGAAGAGGAAAGTGTATTCGCAGTTACTGCTGTTAATGCCAGTGAAAAAACAGTTGTGGAAGCGTTATTTCA    FJJ<FFFAAAJFFFFJJJJJJJJJJJJJJJJJJJJJJJJFJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJFFFAA    AS:i:0    XM:i:0    XO:i:0    XG:i:0    MD:Z:75    NM:i:0    XS:A:+    NH:i:1

You could see field 1 is missing here.

Any idea why this problem?

Note: TopHat v2.0.9

Thank you.