I have cufflinks output from tophat alignments and I want to get the sequences of the transcripts. I've been extracting the sequence from the reference genome, but I'm working in chicken where the reference genome is constructed from the wild type and I'm sequencing a very specialized breed, so I would really like to get the sequences of the transcripts from my RNA-seq data. I've searched around this site and other places and found some solutions like generating vcf files with samtools but they all seem geared towards just getting a single sequence, rather than thousands. I think using a loop with these methods will be extremely slow. Is there any quicker way to get the full set of transcript sequences predicted by cufflinks from the RNA-seq data?
Question: Get transcript sequence from RNA-seq
3.1 years ago by
colin.kern • 340
colin.kern • 340 wrote:
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