Question: Inconsistent Cuffdiff
0
gravatar for i b
6.2 years ago by
i b330
i b330 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 • 1.1k views
ADD COMMENTlink modified 6.2 years ago by Sarah Marcus20 • written 6.2 years ago by i b330
0
gravatar for Sarah Marcus
6.2 years ago by
Sarah Marcus20
Sarah Marcus20 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 COMMENTlink written 6.2 years ago by Sarah Marcus20
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 REPLYlink written 6.2 years ago by Jennifer Hillman Jackson25k
Thanks Jen! That solved my problem. Sarah
ADD REPLYlink written 6.2 years ago by Sarah Marcus20
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