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Old 03-01-2013, 07:02 AM   #1
Bioinformaticsnewb
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Location: North Dakota

Join Date: Nov 2011
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Default cuffmerge output issue

Hi everyone,

I know that there are a variety of questions that have been asked regarding cuffmerge output, but I am having issues with the file sizes in the output. I am currently doing a differential expression analysis on 12 libraries and am trying to run cuffmerge to generate a merged.gtf file for cuffdiff. The program is running and completing, but the size of the merged.gft file is only 128Kb compared to the nearly 40Mb file size for the transcripts.gtf. Has anyone else run into a similar problem?

Thanks,
Alex
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