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Question: TopHat with Culex quinquefasciatus genome
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gravatar for cheolho_sim
22 months ago by
cheolho_sim • 0
cheolho_sim • 0 wrote:

I try to use TopHat for RNA-seq data. The Culex quinquefasciatus genome will be used for the TopHat. Would you me a guide which genome data that I need to use along with RNA-seq data (from Illumina HighSeq)?

Here is the Culex quinquefasciatus genome data webpage. https://www.vectorbase.org/organisms/culex-quinquefasciatus

Assembly, Gene set, Scaffolds?
rna-seq • 516 views
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modified 22 months ago by Jennifer Hillman Jackson ♦ 25k • written 22 months ago by cheolho_sim • 0
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gravatar for Jennifer Hillman Jackson
22 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Use the Scaffolds data as the target reference genome.

Load the fasta file into Galaxy and use it as a Custom reference genome with Tophat and other tools. https://wiki.galaxyproject.org/Support#Custom_reference_genome

Thanks, Jen, Galaxy team
ADD COMMENT • link written 22 months ago by Jennifer Hillman Jackson ♦ 25k
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