CLC vs tophat: differences is alignment?

[newbietonextgen]

Hi

I have been using CLC for sometime and was wondering if any one has compared metrics between CLC and other aligners.

I found something interesting and wanted to know if anybody has observed it. We took some RNA-seq data, 100bp paired end reads, and aligned it using the latest CLC and Tophat. Both were run with defaults with a GTF file for alignment.

We then took 10,000 bp region from both the BAM files and looked at number of reads aligned and the accuracy's of the alignment.

So far, CLC aligns more reads to the same region compared to tophat (11,200/3500). Now coming to the big question of accuracy, we found twice the number of pairs in CLC than tophat (3346 vs 1640 pair). So the question is how is CLC doing it? Mind you it's only one region..

Can test people can suggest that would be very comprehensive or need details of the run.

cheers
newbie

[NextGenSeq]

Every alignment algorithm gives different results.

[newbietonextgen]

True to some extent as i have tried GSNAP vs Tophat vs CLC. But what baffles me are the differences in numbers. What would happen if you are working on depth of coverage data and how would one normalize it to take in account the differences in aligners.