Originally posted by dpryan
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Hi D
I have two samples (i.e. two .fastq files) from bovine. If I want to see whether a sequence (supposed named "GQ2") is expressed in bovine cells. (I have got the FASTA of this sequence) The sequence is unannotated in the current bovine genome, so might not have been tested in the analyses thus far.
Q1: How could I do it?
Q2: My solution (I don't know is it correct)
firstly I generate the bowtie/bowtie2 index of this "GQ2" based on the FASTA sequence, and then map my fastq file to that "GQ2" genome. is it correct?
Thank you!
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