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Question: I can't choose a "reference transcriptome"
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gravatar for HehnlyH
19 months ago by
HehnlyH • 0
HehnlyH • 0 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 • 747 views
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modified 19 months ago by Jennifer Hillman Jackson ♦ 25k • written 19 months ago by HehnlyH • 0
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19 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 19 months ago by Jennifer Hillman Jackson ♦ 25k
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