Hi,
We recently got single end directional mRNA-Seq data obtained using the new Illumina protocol. I'm trying to map it to the genome using TopHat and Cufflinks. For both programs to understand that the library prep was different, I'm using the option
However, I'm not really sure whether the Illumina protocol only does first strand sequencing, or whether the library type should be standard Illumina or fr-secondstrand. I did it both ways (standard and firststrand) and found that the number of transcripts I get after Cufflinks is quite different. I know Illumina uses its own 5' and 3' adapters for defining the strand specificity, but not really clear how it does that/which strand it ends up sequencing?? Is the sequence we get that of the Coding Strand or the Template Strand?
Please help.
Thanks!
We recently got single end directional mRNA-Seq data obtained using the new Illumina protocol. I'm trying to map it to the genome using TopHat and Cufflinks. For both programs to understand that the library prep was different, I'm using the option
Code:
--library-type fr-firststrand
Please help.
Thanks!
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