Question: Extracting nucleotides from genome for gene function determination
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gravatar for sbitterw
4 weeks ago by
sbitterw0
sbitterw0 wrote:

Hello and thank you so much for your time,

I have a database of gene counts and names from HTSeq-count. Each count maps to a CDS sequence named something like "g36525.t1." located in my reference genome. If I search the sequence name within the genome file (GFF3) I find a line that has the sequence's start and stop positions.

How do I extract the raw nucleotide values of this gene from the genome itself? What is the best way of determining gene function from the extracted nucleotides? Is there an easier way to determine gene function for a TagSeq experiment?

Thank you again.

Stephan

tagseq genome gene function • 106 views
ADD COMMENTlink written 4 weeks ago by sbitterw0
1

You can use the gffread utility found here.

ADD REPLYlink written 4 weeks ago by genomax91k
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