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Question: HG38 .gtf file
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gravatar for joseph.andrews
3.1 years ago by
joseph.andrews • 20
Canada
joseph.andrews • 20 wrote:

Hello.

For practise, I am running an RNA-seq analysis on some of the RNA-seq data from Illumina Bodymap 2.0 folder available in the Shared Datasets folder, using the tutorial 5-2,  RNA Sequence Analysis- Assembly Quantitation, and Differential Expression (12-20) video as a guide.  In it, he uses a file called "chr19-annotations.gtf" to annotate, when he runs Cufflinks.  Is there an equivalent .gtf file for hg38 that can be used in the analysis of  Illumina Bodymap 2.0?

Thanks in advance....

 

 
illumina bodymap 2.0 cufflinks rna-seq • 1.7k views
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modified 3.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.1 years ago by joseph.andrews • 20
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gravatar for Jennifer Hillman Jackson
3.1 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Try the hg38 GTF from from iGenomes for best results with the Tuxedo RNA-seq tools:

https://support.illumina.com/sequencing/sequencing_software/igenome.html

Best, Jen, Galaxy team
ADD COMMENT • link written 3.1 years ago by Jennifer Hillman Jackson ♦ 25k

Thanks Jen. I grabbed the UCSC hg38...

Joe Activity on a post you are following on Galaxy Biostar ( http://biostar.usegalaxy.org)

User Jennifer Hillman Jackson ( http://biostar.usegalaxy.org/u/254/) wrote Answer: HG38 .gtf file ( http://biostar.usegalaxy.org/p/14880/#14889) :

Hello, Try the hg38 GTF from from iGenomes for best results with the Tuxedo RNA-seq tools: https://support.illumina.com/sequencing/sequencing_software/igenome.html Best, Jen, Galaxy team

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ADD REPLY • link written 3.1 years ago by joseph.andrews • 20
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