Question: fasta sequence from differential expressed gene
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gravatar for n.sarker
5 months ago by
n.sarker0
n.sarker0 wrote:

Hi, I am Galaxy user. How could I get fasta sequences of differential expressed genes from Galaxy incorporated EdgeR or DeSeq2 programme?

thanks in advance

fasta de galaxy deseq2 edger • 183 views
ADD COMMENTlink modified 5 months ago by Jennifer Hillman Jackson25k • written 5 months ago by n.sarker0
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gravatar for Jennifer Hillman Jackson
5 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

The gene names are assigned from the reference GTF used in upstream steps (when one is used). That GTF will have the genomic coordinates of the transcripts associated with that gene. The tool Extract Genomic DNA using coordinates from assembled/unassembled genomes can be used with a GTF input (and Custom Genome/Transcriptome Build, as needed).

Known gene names (those with a public identifier, not "genes" or "transcript" names auto-assigned by the tools)) can also be used at other sites to directly extract the associated fasta. Where to do this depends on the gene symbol type/name. UCSC supports most types through their Table Browser, but Ensembl, NCBI, and others also have fasta data downloads available.

Tutorials (many RNA-seq include DeSeq2): https://galaxyproject.org/learn/

Support: https://galaxyproject.org/support/

Thanks! Jen, Galaxy team

ADD COMMENTlink written 5 months ago by Jennifer Hillman Jackson25k
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