I am a very beginner of RNA-seq analysis. I had completed the RNA-seq process by following the workflow in the link below; I had used Salmon and tximport:
After this part, I had used Ensembl for transcript annotation, but I only get the names for genes (not for transcripts) as shown below:
- ENSG00000000457 etc.
However, I was asked to detect whether a specific isoform of a given gene is present or not in the samples. The gene is present in the final result table (as an "average" of the present isoforms I assume). However, the result table provided me only with list of genes and not the transcripts, isoforms are not annotated.
It might be a silly question, but is it possible to obtain FASTA format of this desired specific isoform of the given gene and search it into the FASTQ file of the samples? Is it logical? Or could you suggest me a better way? I have the quantification and abundances, maybe I should use another annotation method to obtain transcript IDs but I am not sure about which part I should change. Thanks in advance