I have the data from an RNA-seq experiment, and as a result I have a list of genes with their corresponding number of genes. I have been able to do some filtering and as a result, I have finally a list of 200 genes. For this list, I want to run MEME so as to see if there is anything common motif in their RNA sequences, say in their 5'UTR region.
My question is - Is there a way I can automatically get the whole RNA sequences for all these genes (including the 5' and 3' UTR regions)? I searched on Google, and found this (https://www.ncbi.nlm.nih.gov/guide/howto/find-transcript-gene/) but it will give me results one gene at a time.
EDIT - A friend of mine told me that since I have the RNA-seq data, I can also use
samtools view to find the RNA sequences, by using the bed files. I am not sure I understand this. If anyone has any ideas related to this method, it would be awesome.