Top Hat and library option

Fiki · 06-26-2012, 06:10 AM

I've got a RNA-Seq experiment, whose author said in the paper that used Strand-specific RNA-Seq. Reading the experimental procedures, I've found ,briefly,that they generated first strand and during the second strand synthesis they add dUTP (here the paper).

The problem is when I've to do alignments using TopHat. TopHat documentation says that we've to use fr-firststrand with dUTP, however it says too that we've to use fr-secondstrand when the strand generated during second strand synthesis is sequenced.

any ideas?

Thanks!

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06-26-2012, 06:10 AM	#1
Fiki Junior Member Location: Spain Join Date: Jun 2012 Posts: 3	Top Hat and library option I've got a RNA-Seq experiment, whose author said in the paper that used Strand-specific RNA-Seq. Reading the experimental procedures, I've found ,briefly,that they generated first strand and during the second strand synthesis they add dUTP (here the paper). The problem is when I've to do alignments using TopHat. TopHat documentation says that we've to use fr-firststrand with dUTP, however it says too that we've to use fr-secondstrand when the strand generated during second strand synthesis is sequenced. any ideas? Thanks!