Hi all. Sorry to bother you.
I have a question about Cufflinks suite. Basically, I used Cufflinks to assemble transcripts and genes, then Cuffmerge to merge all the assemblies and generate an annotation and at last Cuffdiff to identify differentially expressed genes. Some genes were marked with HIDATA when using default value of --max-bundle-frags. After increasing the --max-bundle-frags value, there is no gene labled with HIDATA in the gene and transcript assembly step by Cufflinks. However, in Cuffdiff step, I still got HIDATA tag.
Is there any other arguments should be defined in Cuffdiff step?
Wish your help! Thanks very much! I really appreciate it.
I have a question about Cufflinks suite. Basically, I used Cufflinks to assemble transcripts and genes, then Cuffmerge to merge all the assemblies and generate an annotation and at last Cuffdiff to identify differentially expressed genes. Some genes were marked with HIDATA when using default value of --max-bundle-frags. After increasing the --max-bundle-frags value, there is no gene labled with HIDATA in the gene and transcript assembly step by Cufflinks. However, in Cuffdiff step, I still got HIDATA tag.
Is there any other arguments should be defined in Cuffdiff step?
Wish your help! Thanks very much! I really appreciate it.
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