I have some genomic coordinates and I want to retrieve their RNA sequence especially the ones for reverse complement ones (since RNA sequence would not be strand specific). Where could I find such tool or package?
Question: Retrieving RNA sequence from corresponding genomic coordinates
1
Aishwarya Kulkarni • 80 wrote:
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modified 5.8 years ago
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Anima Mundi • 2.8k
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5.8 years ago by
Aishwarya Kulkarni • 80
3
Anima Mundi • 2.8k wrote:
Hello,
you can also go to the UCSC Table Browser (https://genome.ucsc.edu/cgi-bin/hgTables), upload your input file as a custom track ("add custom track" button), select your genome, choose "sequence" as output format, press "get output" and choose "mRNA" from the following menu. This would output your mRNA sequences in FASTA format.
Thanks this is most useful! It's just that I cannot see the mRNA option once I click get sequence, all I get is:
All upper case.
All lower case.
Mask repeats: to lower case to N
Reverse complement (get '-' strand sequence)
0
arnstrm • 1.8k wrote:
See this thread for details:
Extract Cds Fastas From A Gff Annotation + Reference Sequence
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what organism?
Human genome hg19