User: roxy.zhang

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roxy.zhang0
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Posts by roxy.zhang

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Answer: A: Cummerbund visualization of expression plot
... Hello I am having the exact same problem here! I seem to have done everything right but the gene_id part just keep sowing up as null for some reason. Did you guys every get it solved? Thanks a lot! ...
written 9 weeks ago by roxy.zhang0
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Permanently deleted datasets/histories but quota was not updated or is incorrect
... Hello I have deleted a bunch of datasets from my history permanently however, this is not reflected on my history. The number of GBs deleted have not been freed more space in my working quota. Is this a problem in the back end? Thank you! Best, Roxy ...
quota dataset recalculate history account written 10 weeks ago by roxy.zhang0 • updated 10 weeks ago by Jennifer Hillman Jackson22k
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Comment: C: Cuffcompare successful but generate empty files.
... Hi Jen Thank you very much for your prompt replies. I have encountered another problem however. I have permanently deleted some datasets in my history but it is still showing in my work space/ quota? Is it possible for you guys to take a look and perhaps recalculate it? Thanks a lot! Best, Roxy ...
written 10 weeks ago by roxy.zhang0
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CummeRbund input from Cuffdiff output
... Hello All I just finished my Cuffdiff on a set of practice data, and I am planning to visualize my output in CummeRbund, however, it does not seem to accept Cuffdiff output. I find this very strange because in many protocols, CummeRbund is directly after Cuffdiff and it seems to use Cuffdiff outpu ...
cuffdiff rna-seq galaxy cummerbund cufflnks written 10 weeks ago by roxy.zhang0 • updated 10 weeks ago by Jennifer Hillman Jackson22k
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Comment: C: cufflink only assembles 1 transcript for gene of interest when tophat splice jun
... Hello Jen Thank you for your prompt reply! I am using the hg19 as a guide reference genome, and I selected it from galaxy's own source. My data is from Illumina Hiseq. I was thinking of adding more subjects in, maybe that will help? Because I got my data from SRA and the original paper had over 5 ...
written 10 weeks ago by roxy.zhang0
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cufflink only assembles 1 transcript for gene of interest when tophat splice junctions suggest different alternative splicings
... Hello Friends I am currently doing RNA-seq hoping to find new transcript (we found with our qPCR, other lab also found though experimentally induced) and to quantify them. My tophat splice junction results (viewed on IGB) displayed splice junctions that suggest different alternative splicing. Howe ...
cufflink tophat rna-seq written 10 weeks ago by roxy.zhang0 • updated 10 weeks ago by Jennifer Hillman Jackson22k
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Cuffcompare successful but generate empty files.
... Hello friends I am currently doing RNA-seq for 3 datasets (obtained publicly through NCBI-SRA), each dataset is for 1 individual and all three individuals have different conditions. (c9ALS, sALS, Control). I have successfully ran tophat, and cufflinks. I am now trying to use Cuffcompare/ cuffmer ...
galaxy cuffcompare cufflinks rna-seq written 11 weeks ago by roxy.zhang0 • updated 10 weeks ago by Jennifer Hillman Jackson22k

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