Re: [galaxy-dev] cuffdiff output: FPKM value zero
Hi Suzan, The problem here is that there's an absence of data for one of the genes you want to compare, so one can't really assign any significance to that particular gene or transcript. This would require inventing a singificance value where if a gene is highly expressed in one sample, but not measured at all in another, then that gene should be said to be significantly differentially expressed. If you are looking for situations like this I see no reason why you can't create a rule for identifying them and pulling them out of the cuffdiff results. Even then, you'll have to make some decision about what FPKM value would be significantly different from 0 in another. Hope this helps. Graham Dr. Graham Etherington Bioinformatics Support Officer, The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH. UK Tel: +44 (0)1603 450601 On 07/09/2012 16:16, "suzan katie" wrote: > > > >Hello everyone, > >I am comparing two samples (control and treated) paired end RNA Seq data. >In the cuffdiff output I have noticed that few genes have zero FPKM value >in one sample and other sample has significant FPKM value. > >I want to identify uniquely expressed genes identified only in one sample >(either control or treated). > > >My question: If something is measured with significance in one sample >(high FPKM), but not measured at all in another sample (Zero FPKM), >should I consider that gene as significant? > >Can anyone explain this. > >Thanks > >suz > > > > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] cuffdiff output: FPKM value zero
Hello everyone, I am comparing two samples (control and treated) paired end RNA Seq data. In the cuffdiff output I have noticed that few genes have zero FPKM value in one sample and other sample has significant FPKM value. I want to identify uniquely expressed genes identified only in one sample (either control or treated). My question: If something is measured with significance in one sample (high FPKM), but not measured at all in another sample (Zero FPKM), should I consider that gene as significant? Can anyone explain this. Thanks suz ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] cuffdiff output
Hello Susan The tool is using the identifier in the "gene_id" attribute from the reference annotation GTF to name the output. This link at the tool manual can help: http://cufflinks.cbcb.umd.edu/howitworks.html#hdif The iGenomes dataset may be what you are looking for. "Shared Data -> Data Libraries -> iGenomes" has the mm9 gene.gtf file loaded already. Other genomes will be added near term. Example of mm9 iGenomes GTF (note that gene_id is the gene symbol): chr1 unknown exon 3204563 3207049 . - . gene_id "Xkr4"; transcript_id "NM_001011874"; gene_name "Xkr4"; p_id "P2739"; tss_id "TSS1881"; For now, you can download and open the archive yourself (locally), then load just the genes.gtf file to Galaxy, if your genome is in the list. http://cufflinks.cbcb.umd.edu/igenomes.html Best, Jen Galaxy team On 8/17/12 6:42 AM, suzan katie wrote: Hello, I am new to using Galaxy tools. I am running paired end RNA-Seq data on Galaxy and I want to differential gene expression between control and treated samples I was fine until running TopHat output, I am having problems with cufflinks and cuffdiff output. I ran the cufflinks and cuffdiff twice, once with reference annotation and once without reference annotation (Imported form UCSC). Output with reference annotation produced output with gene ids naming usc## Output without reference annotation produced output with gene ids naming CUFF1.### Can anyone suggest how to get gene names instead of just numbers? Thanks suz ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] cuffdiff output
Hello, I am new to using Galaxy tools. I am running paired end RNA-Seq data on Galaxy and I want to differential gene expression between control and treated samples I was fine until running TopHat output, I am having problems with cufflinks and cuffdiff output. I ran the cufflinks and cuffdiff twice, once with reference annotation and once without reference annotation (Imported form UCSC). Output with reference annotation produced output with gene ids naming usc## Output without reference annotation produced output with gene ids naming CUFF1.### Can anyone suggest how to get gene names instead of just numbers? Thanks suz ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Cuffdiff output
Hi, I have ran Cuffdiff and got output files: transcript differential expression testing, gene differential expression testing. Could you please tell me how to get the significant differential expression gene and transcript ? Thanks, This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments). ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
