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User: mat12

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mat12 • 10
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Posts by mat12

<prev • 7 results • page 1 of 1 • next >
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Download for reference annotation file (gtf) for NOD/ShiltJ mouse
... Hi, I am in desperately looking for a reference annotation file (gtf) for the NOD/ShiltJ mouse so that I may run Cuffmerge. I cannot find one in gtf format. Help would be very, very, very much appreciated! Thanks, Michelle   ...
cuffmerge reference annotation file gtf rna-seq written 3.1 years ago by mat12 • 10
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Comment: C: Issue running Cuffdiff using Cuffmerge gtf output
... Did you upload replicates for your conditions? Run Cufflinks on each of your replicates and merge them all together in Cuffmerge. This way Cuffdiff has more alignments to work with. Let me know if that works for you! ...
written 3.3 years ago by mat12 • 10
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Comment: C: Issue running Cuffdiff using Cuffmerge gtf output
... Hi Jen, After uploading my replicates I no longer have an issue with Cuffdiff. I am now having issues with my reference annotation because my Cuffdiff output file lists chromosome locations.. but not gene names. Were you suggesting that I input an iGenomes GTF reference dataset as a "reference ann ...
written 3.3 years ago by mat12 • 10
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Cuffdiff issues: test_stat = -nan
... Hi, When I ran Cuffdiff, I had 92 genes that had the problems with the "test_stat" column. These genes had "-nan" for their test_stat value. All of these had log2(fold_change) values equal to either infinity or -infinity. 1. What does mean? 2. Can I trust the significance tests for these genes e ...
cuffdiff fold change test stat cufflinks rna-seq written 3.3 years ago by mat12 • 10
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Cuffdiff issues: test_stat = -nan
... Hi, When I ran Cuffdiff, I had 92 genes that had the problems with the "test_stat" column. These genes had "-nan" for their test_stat value. All of these had log2(fold_change) values equal to either infinity or -infinity. 1. What does mean? 2. Can I trust the significance tests for these genes e ...
cuffdiff fold change test stat cufflinks rna-seq written 3.3 years ago by mat12 • 10
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Answer: A: Issue running Cuffdiff using Cuffmerge gtf output
... Hi Jennifer, Thanks for the reply. I am using the public server http://usegalaxy.org. If you have any more advice I would greatly appreciate it! I will try including the reference dataset that you recommended. Thanks! ...
written 3.3 years ago by mat12 • 10
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Issue running Cuffdiff using Cuffmerge gtf output
... I am trying to use Cuffdiff to find significant changes in mRNA transcript expression between two conditions (1. silenced gene, 2. overexpressed gene) but for some reason have been having difficulties using the Cuffmerge output gtf as input into Cuffdiff. This seems to be a basic question with most ...
cuffdiff cufflinks cuffmerge alignment rna-seq written 3.4 years ago by mat12 • 10

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