Tophat 2 renaming the read IDs after mapping

[mparida85]

Hi All
I am using TopHat v2.0.9.
After mapping and getting the alignment file .bam I find this following issue:

Reads in fastq file:
@HISEQ:77:C4M7KACXX:1:1210:2186:10364 1:N:0:ATCACG
TGACCAGTATTTACTACACGGAGCGTCGTTGAAGTCCCCGAGTCTGTAACGAATGCATTCTTCGACTCCTTGAGCGTCATTTGGCTCGTCA
+
HFHJJJJFFHIJIJJJJJJIIGJJJIFHIJJJJJIIJJJIIHHHHHFFFFFDDDDDDEEDEEDDD?BDDDDDDCCDDDDDDEACDDDDBBB

@HISEQ:77:C4M7KACXX:1:1210:2156:10434 1:N:0:ATCACG
TCTGAGACAGAGGTGAAGTTCCAGTCGGAGATTTGGTGCTGGATACGACCGTTACCGTAAGAGGCAGCGAAAATTCGAGCGTCGTAGGTGT
+
HHHJJJJIJJJJJCHJIIJJJJJJHIJIHIHIJJIIHIJJJJIIIIJJIJHHHFFFDDDDBDCDDBDDDDDDDDDDDECDDDBB<BDDCC@

Reads in bam file:

HISEQ:77:C4M7KACXX:1:1210:2186:10364 73 scaffold_183 916 50 91M * 0 0 TCTGAGACAGAGGTGAAGTTCCAGTCGGAGATTTGGTGCTGGATACGACCGTTACCGTAAGAGGCAGCGAAAATTCGAGCGTCGTAGGTGT HHHJJJJIJJJJJCHJIIJJJJJJHIJIHIHIJJIIHIJJJJIIIIJJIJHHHFFFDDDDBDCDDBDDDDDDDDDDDECDDDBB<BDDCC@ AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:91 YT:Z:UU NH:i:1

HISEQ:77:C4M7KACXX:1:1210:2186:10364 83 scaffold_18 355289 50 91M = 355221 -159 TGACGAGCCAAATGACGCTCAAGGAGTCGAAGAATGCATTCGTTACAGACTCGGGGACTTCAACGACGCTCCGTGTAGTAAATACTGGTCA BBBDDDDCAEDDDDDDCCDDDDDDB?DDDEEDEEDDDDDDFFFFFHHHHHIIJJJIIJJJJJIHFIJJJGIIJJJJJJIJIHFFJJJJHFH AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:91 YT:Z:UU NH:i:1

Read IDs are getting substituted for no reason.
This makes no sense.
Rocky

[mparida85]

Ok so TopHat 2.0.10 release 11/13/2013 claims :
Fixed a bug that could sometimes incorrectly rename the reads in the output alignments.
I am going to give this a try and repost again for anyone who is interested.

[mparida85]

TopHat v2.0.13 fixed this issue.