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Question: Retrieving RNA sequence from corresponding genomic coordinates
1
gravatar for Aishwarya Kulkarni
5.8 years ago by
Aishwarya Kulkarni • 80
United States
Aishwarya Kulkarni • 80 wrote:

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?
rna-seq • 1.6k views
ADD COMMENT • link •
modified 5.8 years ago by Anima Mundi • 2.8k • written 5.8 years ago by Aishwarya Kulkarni • 80

what organism?

ADD REPLY • link written 5.8 years ago by Neilfws ♦ 49k

Human genome hg19
 

ADD REPLY • link written 5.8 years ago by Aishwarya Kulkarni • 80
3
gravatar for Anima Mundi
5.8 years ago by
Anima Mundi • 2.8k
Italy
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.
ADD COMMENT • link modified 5.8 years ago • written 5.8 years ago by Anima Mundi • 2.8k

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) 

ADD REPLY • link modified 5.8 years ago • written 5.8 years ago by Aishwarya Kulkarni • 80
1

I see, then you can create an intersection with "mRNA and EST" (track "Human RNAs"), either to retrieve just the sequences overlapping between your data and human mRNAs, or also to get the complete mRNA sequences with at least partial overlap with your custom track.

ADD REPLY • link modified 5.8 years ago • written 5.8 years ago by Anima Mundi • 2.8k
0
gravatar for arnstrm
5.8 years ago by
arnstrm • 1.8k
Ames, IA
arnstrm • 1.8k wrote:

See this thread for details:

Extract Cds Fastas From A Gff Annotation + Reference Sequence

 
ADD COMMENT • link written 5.8 years ago by arnstrm • 1.8k
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