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Question: GTF for hg18
1
gravatar for jacox
16 months ago by
jacox • 10
jacox • 10 wrote:

Hi

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.

Thanks
tophat gtf cuffdiff • 403 views
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modified 16 months ago by Jennifer Hillman Jackson ♦ 25k • written 16 months ago by jacox • 10
0
gravatar for Jennifer Hillman Jackson
16 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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 COMMENT • link written 16 months ago by Jennifer Hillman Jackson ♦ 25k
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