Question: TopHat aligning with ensembl in Galaxy
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gravatar for michael.flower.14
2.1 years ago by
michael.flower.1410 wrote:

I'm using the Galaxy interface to analyse RNAseq data. I've successfully aligned using the default reference genome, then counted using the gtf file downloaded from UCSC, then done the differential expression analysis with DeSeq2, which gives good results. I wanted to compare against the ensemble reference genome, but am struggling. I downloaded the DNA FASTA from here - http://www.ensembl.org/info/data/ftp/index.html - but can't get TopHat to align with it. Any help would be much appreciated

ADD COMMENTlink modified 2.1 years ago by Jennifer Hillman Jackson25k • written 2.1 years ago by michael.flower.1410
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gravatar for Jennifer Hillman Jackson
2.1 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

Help for using a custom reference genome is here: https://wiki.galaxyproject.org/Support#Custom_reference_genome

Best, Jen, Galaxy team

ADD COMMENTlink written 2.1 years ago by Jennifer Hillman Jackson25k
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