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Question: Gff3 not recognised by cufflinks
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gravatar for h.stotz
3.0 years ago by
h.stotz • 20
European Union
h.stotz • 20 wrote:

I am trying to use cufflinks, but it does not recognise my reference annotation.  I have a gff3 flile in my history.  So, it should be recognised.  The fasta file on the genome has been uploaded and covers all of the genome sequence.  I notice that there is a run of NNNNNNNNs at the beginning of the first chromosome.  Would that cause problems?

Thanks,

Henrik
galaxy • 668 views
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modified 3.0 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.0 years ago by h.stotz • 20
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gravatar for Jennifer Hillman Jackson
3.0 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Please double check that the datatype assignment has been made and if not, assign it: Support#Tool_does not_recognize_dataset

The start or middle of chromosomes for many genomes consists of a fixed set of ambiguous base calls. These represent chromatin regions. This does not negatively impact analysis.

Thanks, Jen, Galaxy team

 
ADD COMMENT • link written 3.0 years ago by Jennifer Hillman Jackson ♦ 25k
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