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?
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i would appreciate if someone could give an appropriate answer!
Thanks in advance! -
I heard from a talk given by Illumina, casava is good for reads length <= 50.Comment
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The Illumina pipeline will only look for known splice junctions, while TopHat can (at least in theory) find novel splice junctions.Comment
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Hi kopi-o,Originally posted by kopi-o View Post
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.Comment
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Hi kopi-o,
Thanks for highlighting the difference on splice junction prediction between Illumina-Eland and TopHat.Comment
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