hi, i want to start working on a gene for which more than 10 splice varients are shown on ensembl. Fortunately i have access to the BAM file of transcriptome mapped, using STAR, RNA seq data from the cells which i will be using for my experiment. Thus i wanted to know is there a way through which i can get the sequence(Fasta file) of the transcript which is present in my cells of interest?
My expertise is in the wet lab but I have some knowlwge of both Python and R. So if any package is available in these will be suitable for me. and could you please tell me computational capacity that will be needed so that i can perform it on proper system. Thanks a lot for your help
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