FASTA sequences extraction
How to extract FASTA sequences for novel transcripts?
fasta
sequences
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Roy.anupama11 •
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Could you elaborate a bit the question? How did you predict those novel transcripts? What is the information you have about those novel transcripts?
I got the GTF file using stringtie having the start and end of each novel transcripts. How to extract the start and end for each transcripts and then the FASTA?