Question: How to include ensembl Human annotation FASTA files in Galaxy for cufflinks bias correction
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gravatar for karyna_schmidt
3.5 years ago by
United States
karyna_schmidt0 wrote:

Hi everyone!

I am working on an RNAseq project and have successfully run cufflinks using the Ensembl Homo_sapiens.GRCh37.75 GTF file. In order to run cufflinks, however, I had to turn off the bias correction. If I want to include the bias correction in my analysis, do I need to import the Ensembl FASTA files? If so, is there an easy way to retrieve these files through Galaxy?

My understanding is that once the Bias Correction is turned to YES, I will need to specify if the FASTA files are locally cached or in my history. Is it correct that I select history only if I upload the FASTA files manually?

Any help is greatly appreciated!

 

ensembl galaxy rna-seq cufflinks • 1.3k views
ADD COMMENTlink modified 3.5 years ago by Jennifer Hillman Jackson23k • written 3.5 years ago by karyna_schmidt0
0
gravatar for Jennifer Hillman Jackson
3.5 years ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

Yes, the same exact version of the reference genome must be used for all steps in an analysis. The identifiers can be mapped between the different versions and altered using various methods, but this is most often done at the start of an analysis. 

http://wiki.galaxyproject.org/Support#Reference_genomes
http://wiki.galaxyproject.org/Support#Custom_reference_genome

If you have memory problems due to the size of the genome, consider a Cloud Galaxy:
http://usegalaxy.org/cloud

Take care, Jen, Galaxy team

ADD COMMENTlink written 3.5 years ago by Jennifer Hillman Jackson23k
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