Question: I can't choose a "reference transcriptome"
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gravatar for HehnlyH
8 months ago by
HehnlyH0
HehnlyH0 wrote:

I'm trying to use Salmon Transcript quantification and I can't choose a reference transcriptome. I have chosen a FastQ Groomer data set. I'm very new to looking at RNA seq data.

rna-seq • 276 views
ADD COMMENTlink modified 8 months ago by Jennifer Hillman Jackson23k • written 8 months ago by HehnlyH0
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gravatar for Jennifer Hillman Jackson
8 months ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

The fasta reference transcriptome should have the datatype "fasta" assigned for the tool to recognize the input.

Here is help for correct fasta formatting for datasets used as Custom reference genomes/transcriptomes. Many mapping tools are not picky about the format, yet many downstream tools are. It is generally a good idea to ensure correct formatting as part of the prep stages before starting any analysis that uses a custom genome/transcriptome.

We hope this helps! Jen, Galaxy team

ADD COMMENTlink written 8 months ago by Jennifer Hillman Jackson23k
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