Question: GTF for hg18
gravatar for jacox
7 months ago by
jacox10 wrote:


I have tried to run Cuffdiff on tophat samples based on the hg18 reference genome. I imported the genome from the UCSC genome browser. However whenever I try to run the cuffdiff I always get the error sort order of reads in BAMs must be the same. Could anyone provide me with the hg18 genome in gtf format so I can get past this issue, or give me another way to solve it.


tophat gtf cuffdiff • 183 views
ADD COMMENTlink modified 7 months ago by Jennifer Hillman Jackson24k • written 7 months ago by jacox10
gravatar for Jennifer Hillman Jackson
7 months ago by
United States
Jennifer Hillman Jackson24k wrote:


You can use the GTF from UCSC or iGenomes for hg18 but both often benefit from a sort, as well as the input BAMs (depending on the mapper used).

Thanks! Jen, Galaxy team

ADD COMMENTlink written 7 months ago by Jennifer Hillman Jackson24k
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