User: cookseq2

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cookseq20
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Posts by cookseq2

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Answer: A: Locally cached sequence not detected from DBkey in cuffmerge when using mm10
... The only workaround i have found for this problem involves clicking on the 'rerun job again' button on a CuffDiff run in which the sequence data could be found. Though i did this for hg19 i don't think there would be any difference if you needed to use mm10. I hope this helps. ...
written 3.3 years ago by cookseq20
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Answer: A: Locally cached sequence not detected from DBkey in cuffmerge when using mm10
... Can you use a FASTA reference file instead of the locally cached sequence data, as unfortunately the locally cached sequence data is still unavailable.    Richard Hogg ...
written 3.3 years ago by cookseq20
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CuffDiff and normalization between runs
... Dear All! I am currently conducting an RNA-Seq experiment in which i have several samples (1 normal sample, 2 cancer samples and 2 cancer + virus samples). I have used cuffdiff to produce datasets for each of these samples vs the normal sample and use these results to check for differences in gene ...
galaxy cufflinks rna-seq written 3.3 years ago by cookseq20
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Comment: C: TopHat run starting then stopping
... FYI this work has been done on the main public galaxy server, i will attempt to download the datasets and retry the analysis on the galaxy test server and see if the jobs resolve on there. ...
written 3.3 years ago by cookseq20
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Comment: A: TopHat run starting then stopping
... The jobs were first submitted on Thursday the 11th of June ...
written 3.3 years ago by cookseq20
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TopHat run starting then stopping
... Dear Galaxy Team I have been having a problem with some tophat runs on my galaxy account. When originally submitted these jobs began to run almost immediately but were grayed out the morning after. It is a paired end tophat alignment on two large datasets (around 17GB) and i know that jobs which ar ...
galaxy alignment tophat written 3.3 years ago by cookseq20 • updated 3.3 years ago by Martin Čech ♦♦ 4.9k

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