Hi everyone,
I'm running Cufflinks (v 0.9.3) on one of my datasets (human, 50 bp PE, around ~600-700 million reads), and tried to assemble transcripts without prior annotation.
For the most part, the program works very well. However, when genes adjacent to one another (intergenic distance on the order of a small/medium-sized intron) are the same strand, Cufflinks merge multiple genes into one transcript. I've attached a picture of this example, where DVL2 & PHF23 are both part of the same Cufftranscript.
Would anyone have any recommendations to fix this or reduce the chances of it happening? Since the intergenic distance is short, tweaking the "max-intron-length" flag in Cufflinks probably won't help here.
Thanks!
I'm running Cufflinks (v 0.9.3) on one of my datasets (human, 50 bp PE, around ~600-700 million reads), and tried to assemble transcripts without prior annotation.
For the most part, the program works very well. However, when genes adjacent to one another (intergenic distance on the order of a small/medium-sized intron) are the same strand, Cufflinks merge multiple genes into one transcript. I've attached a picture of this example, where DVL2 & PHF23 are both part of the same Cufftranscript.
Would anyone have any recommendations to fix this or reduce the chances of it happening? Since the intergenic distance is short, tweaking the "max-intron-length" flag in Cufflinks probably won't help here.
Thanks!
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