Hello,
I have the following question:
My RNA library is non-strand specific, and I first aligned it using TopHat. Now I want to estimate abundance of transcripts using Cufflinks and a supplied GTF file of transcripts, but I don't know if in the following scenario I will get the correct estimations:
If read X mapped to the genome at 1-75 on strand - , and on the GTF file there is a transcript at locus 1-100 but on strand + , will Cufflinks assign this read towards the abundance estimation of the transcript?
Thanks for your input,
Carmen
I have the following question:
My RNA library is non-strand specific, and I first aligned it using TopHat. Now I want to estimate abundance of transcripts using Cufflinks and a supplied GTF file of transcripts, but I don't know if in the following scenario I will get the correct estimations:
If read X mapped to the genome at 1-75 on strand - , and on the GTF file there is a transcript at locus 1-100 but on strand + , will Cufflinks assign this read towards the abundance estimation of the transcript?
Thanks for your input,
Carmen