inconsistent cuffdiff
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
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
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?: <Use one from the history> 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 On 8/21/12 12:21 PM, Sarah Marcus 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 ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
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-- Jennifer Jackson http://galaxyproject.org
Thanks Jen! That solved my problem. Sarah On 8/22/2012 10:59 AM, Jennifer Jackson wrote:
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?: <Use one from the history>
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
On 8/21/12 12:21 PM, Sarah Marcus 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 ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
participants (3)
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i b -
Jennifer Jackson -
Sarah Marcus