Get read counts from transcripts within a text file comparing to a reference transcriptome
I am trying to determine which transcripts in a list have the highest fold change when compared to a reference transcriptome. I cannot figure out a way to input a text file containing the transcript name + sequence (~500 transcripts), compare it to a reference transcriptome (fasta file), and return the ranking of transcripts based on fold change.
Let me know if you have any ideas. Thanks.
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