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Question: Inconsistent Cuffdiff
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gravatar for i b
6.3 years ago by
i b • 330
i b • 330 wrote:
dear all these are the cuffdiff outputs for the same transcript/gene (one isoform only): transcript differential expression value1 value2 log2fold test stat pvalue q value significant 18.8175 114.371 2.60357 -2.88358 0.00393177 0.0630024 no gene differential expression value1 value2 log2fold test stat pvalue q value significant 18.8175 114.371 2.60357 -2.88358 0.00393177 0.0397768 yes how could be that the gene expression in significnat but the transcript is not?all the values are the same, but the q values changes.Please explani!!I 'm really concerned about how cuffdiff makes these calculation! thanks ib
rna-seq cuffdiff • 1.2k views
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modified 6.3 years ago by Sarah Marcus • 20 • written 6.3 years ago by i b • 330
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gravatar for Sarah Marcus
6.3 years ago by
Sarah Marcus • 20
Sarah Marcus • 20 wrote:
Dear All, I was wondering if it would be possible to add Mycobacterium tuberculosis H37Rv as a reference genome to the list of built-in indexes in the Map with Bowtie for Illumina (version 1.1.2) tool. Thank you, Sarah
ADD COMMENT • link written 6.3 years ago by Sarah Marcus • 20
Hello Sarah, We can add this genome to the list to be indexed for Bowtie. Meanwhile, quickest way to work with small genomes immediately is as a custom genome. Simply load the genome into your history in fasta format and start using it with tools, including Bowtie. Just set these options to get started: Will you select a reference genome from your history or use a built-in index?: Select the reference genome: <pick the="" dataset="" containing="" genome=""> http://wiki.g2.bx.psu.edu/Support#Custom_reference_genome http://wiki.g2.bx.psu.edu/Learn/CustomGenomes Thanks! Jen Galaxy team -- Jennifer Jackson http://galaxyproject.org
ADD REPLY • link written 6.3 years ago by Jennifer Hillman Jackson ♦ 25k
Thanks Jen! That solved my problem. Sarah
ADD REPLY • link written 6.3 years ago by Sarah Marcus • 20
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