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Hi Guys,
I'm doing a fungus RNA-Seq.However, the merged transcriptome gave me very long transcripts (generally >2K). I used GeneMarES to do some sampling prediction, and found cases that contain more than one ORF in a transcript.
Some professors suggested because Tophat/Cufflinks was designed for human genome, the default of transcript length and intron length is longer than fungus.
I appreciate some commends about how do you think about it. Because I didn't see any paper mentioned about how they adjusted the parameters to fit their organism. Does adjust parameters a general way to do? Or anyone suggests to stick with default?
And if anyone could share your experience on adjusting parameters/options in Tophat/Cufflinks, I'll appreciate.
I'm doing a fungus RNA-Seq.However, the merged transcriptome gave me very long transcripts (generally >2K). I used GeneMarES to do some sampling prediction, and found cases that contain more than one ORF in a transcript.
Some professors suggested because Tophat/Cufflinks was designed for human genome, the default of transcript length and intron length is longer than fungus.
I appreciate some commends about how do you think about it. Because I didn't see any paper mentioned about how they adjusted the parameters to fit their organism. Does adjust parameters a general way to do? Or anyone suggests to stick with default?
And if anyone could share your experience on adjusting parameters/options in Tophat/Cufflinks, I'll appreciate.