Question: Cufflink on RNA-seq
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gravatar for zhangtianliu92
9 months ago by
zhangtianliu920 wrote:

What difference betwen reference annotation file and reference genome file on cufflinks? And how to gain reference annotation file on cufflink?

rna-seq • 228 views
ADD COMMENTlink modified 9 months ago by Jennifer Hillman Jackson24k • written 9 months ago by zhangtianliu920
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gravatar for Jennifer Hillman Jackson
9 months ago by
United States
Jennifer Hillman Jackson24k wrote:

Hello,

  • Reference annotation = GTF, GFF, BED, Tabular or other = Describes what, and usually where, genomic features are located on a specific genome build. Features can be representative of transcripts, genes, transcription start sites, SNPs, and much (much) more.

  • Reference genome = Fasta = Describes the nucleotide content of a specific genome build (ATCGN). There are protein versions of this type of data but then the answer becomes more complicated. When doing RNA-seq analysis with these tools, you reference genome/transcriptome/exome will be in nucleotide format.

This prior Q&A explains the difference in the context of a specific question including potential sources. Consider the mm10 database (mouse) as an example to be replaced with your target genome. https://biostar.usegalaxy.org/p/22862

This troubleshooting help for data mismatch problems between reference annotation/genomes inputs is another good resource. And might be helpful later on. Choosing input data that is all based on the same reference genome build is very important. https://galaxyproject.org/support/chrom-identifiers/

Let us know if you have questions that were not covered or are unclear, Jen, Galaxy team

ADD COMMENTlink written 9 months ago by Jennifer Hillman Jackson24k
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