Question: Retrieving RNA sequence from corresponding genomic coordinates
1
gravatar for Aishwarya Kulkarni
5.8 years ago by
United States
Aishwarya Kulkarni80 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 COMMENTlink modified 5.8 years ago by Anima Mundi2.8k • written 5.8 years ago by Aishwarya Kulkarni80

what organism?

ADD REPLYlink written 5.8 years ago by Neilfws49k

Human genome hg19
 

ADD REPLYlink written 5.8 years ago by Aishwarya Kulkarni80
3
gravatar for Anima Mundi
5.8 years ago by
Anima Mundi2.8k
Italy
Anima Mundi2.8k 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 COMMENTlink modified 5.8 years ago • written 5.8 years ago by Anima Mundi2.8k

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 REPLYlink modified 5.8 years ago • written 5.8 years ago by Aishwarya Kulkarni80
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 REPLYlink modified 5.8 years ago • written 5.8 years ago by Anima Mundi2.8k
0
gravatar for arnstrm
5.8 years ago by
arnstrm1.8k
Ames, IA
arnstrm1.8k wrote:

See this thread for details:

Extract Cds Fastas From A Gff Annotation + Reference Sequence

 

ADD COMMENTlink written 5.8 years ago by arnstrm1.8k
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