Where to file data for RNA-seq workflow: gene-level exploratory analysis and differential expression?
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anamarija ▴ 10
@anamarija-22787
Last seen 16 months ago

Hello,

I am trying to follow this tutorial: https://www.bioconductor.org/packages/devel/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html

and under: 2.2 Quantifying with Salmon they mentions this dataset:

DATASETS = ["SRR1039508",
            "SRR1039509",
            "SRR1039512",
            "SRR1039513",
            "SRR1039516",
            "SRR1039517",
            "SRR1039520",
            "SRR1039521"]

they also mention: "a short tutorial on how to use Salmon can be found here, so instead we will provide the code that was used to quantify the files used in this workflow"

in Salmon tutorial: https://combine-lab.github.io/salmon/getting_started/ under: Obtaining sequencing data data looks like this: DRR016125...

Can I assume that I can use these files downloaded for Salmon tutorial for the above tutorial, in other words can I use say DRR016125 instead of SRR1039508 above etc?

Also how do I determine what is for my original Human data the appropriate gencode file from here:https://www.gencodegenes.org/human/

Thanks Ana

rna-seq • 163 views
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@kevin
Last seen 11 hours ago
South Africa

Hello Ana,

The 'DRR' data s obviously from Arabidopsis thaliana, while the 'SRR' files that are mentioned are from Homo sapiens. The tutorials can be used for any species, assuming that you are matching on the species of origin, which includes matching the raw data, the reference transcriptome, and any GTF that you may use.

Also how do I determine what is for my original Human data the appropriate gencode file from here:https://www.gencodegenes.org/human/

For your reference transcriptome, for the vast majority of use cases, you will want to use:

  • Fasta files --> Protein-coding transcript sequences

Kevin

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