Get read counts from transcripts within a text file comparing to a reference transcriptome

Question

[julianneradford]

Hi there,

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.

[Istvan Albert]

what tools/technique/methodology do you have in mind?