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Old 07-08-2011, 03:47 AM   #1
blue mood
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Location: China

Join Date: Jul 2011
Posts: 22
Red face tophat/bowtie version difference

Hi,everyone!
I am mapping some 90bp Solexa RNA-Seq reads to the genome.
I have used two versions of tophat.when i use tophat-1.0.12(bowtie-0.12.5),i get about 77% mapped reads, but it becomes 68% with tophat-1.3.1(bowtie-0.12.7).when i check the sam file,i found that in the newer version,reads with 75M which will be outputed were lost,only the 90M ones were outputed. I am confused because i used the same arguments ' -g 10 -r 20 --solexa1.3-quals '.
B81EPKABXX:2:1202:2022:89951#ACTTGAAT 177 C157522184 8 255 75M = 12 0
B81EPKABXX:2:1101:1963:25916#ACTTGAAT 137 C157522184 15 255 75M * 0 0

B81EPKABXX:2:1101:2225:8227#ACTTGAAT 99 C157993127 73474 255 90M = 73585 201
B81EPKABXX:2:1101:11095:89673#ACTTGAAT 153 C157998321 5 255 90M * 0 0

The former two reads are result of tophat-1.0.12 and the later two ones are result of tophat-1.3.1 .
So anyone knows the possible reasons?
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