Difference between TopHat and Illumina-CASAVA

[ParthavJailwala]

We are analyzing illumina 75bp paired-end RNA-seq data. For mapping, what are the key differences between TopHat and Illumina's eland-CASAVA pipeline for RNA-seq data?

[sphil]

i would appreciate if someone could give an appropriate answer!
Thanks in advance!

[arrchi]

I heard from a talk given by Illumina, casava is good for reads length <= 50.

[kopi-o]

The Illumina pipeline will only look for known splice junctions, while TopHat can (at least in theory) find novel splice junctions.

[ParthavJailwala]

The Illumina pipeline will only look for known splice junctions, while TopHat can (at least in theory) find novel splice junctions.

Hi kopi-o,

Thanks for highlighting that difference.

One other difference could be the no. of basepairs that the algorithm expects as the 'seed' in order to generate accurate alignments. For illumina-eland, I know it is 32bp, but not sure what seed length does TopHat expect.

[ParthavJailwala]

Hi kopi-o,

Thanks for highlighting the difference on splice junction prediction between Illumina-Eland and TopHat.