Dear all,
I need to quantify the expression value for several transcripts that are not annotated in standard ENSEMBL genomes after I have aligned the reads to reference genome/transcriptome and quantified the gene/transcript expression level.
I think I should combine the unannotated transcripts with the reference genome, and then map all reads to the reference genome/transcriptome, instead of only map reads to the unannotated transcripts. Am I right? Or is there any other ways to quantify those annotated transcripts?
And I don't have gtf file for the unannotated transcripts. I only have the sequences and RefSeq ID of those transcripts. So another question is: how to generate gtf file for the unannotated transcripts?
Thanks a lot in advance.
I need to quantify the expression value for several transcripts that are not annotated in standard ENSEMBL genomes after I have aligned the reads to reference genome/transcriptome and quantified the gene/transcript expression level.
I think I should combine the unannotated transcripts with the reference genome, and then map all reads to the reference genome/transcriptome, instead of only map reads to the unannotated transcripts. Am I right? Or is there any other ways to quantify those annotated transcripts?
And I don't have gtf file for the unannotated transcripts. I only have the sequences and RefSeq ID of those transcripts. So another question is: how to generate gtf file for the unannotated transcripts?
Thanks a lot in advance.
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