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  • #16
    Thank you so much for this! I will give it a try and hopefully be able to complete cuffdiff after this!

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    • #17
      Still stuck at 99%

      Mallela,

      Unfortunately, it appears that my cuffdiff run is stuck at 99% again. I performed the markduplicates run just fine for all of my samples, then ran through cufflinks and cuffmerge with the new reads. I allowed cuffdiff to run overnight and it has stopped at the same point that it was stuck at yesterday. Do you have any other recommendations?

      Lauren

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      • #18
        how about you try inserting this extra option into your picard command ?
        Code:
        REMOVE_DUPLICATES=true

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        • #19
          Originally posted by mallela View Post
          how about you try inserting this extra option into your picard command ?
          Code:
          REMOVE_DUPLICATES=true
          Btw, can you paste me your recent cuffdiff command that you have used after you have marked the duplicates? Did you use the *_md.bam files?

          Why don't you try using cuffquant on your *_md.bam files and then use the cuffdiff on the resultant *.cxb files ? The cufflinks site says that it will speed up the process.

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