Hi everyone,
I used tophat and cufflinks to assemble RNA-seq data. The result is good when the reads coverage is high. But I am confused the result when reads coverage is low. I attatched an example
11.pdf
why the exons identified by cufflinks is divided into 5 pieces ? I think they should conbimed into 2 exons according to the comparison of gene models, and it also seems ignore the junction information identified by tophat. Does anyone have some ideas
I used tophat and cufflinks to assemble RNA-seq data. The result is good when the reads coverage is high. But I am confused the result when reads coverage is low. I attatched an example
11.pdf
why the exons identified by cufflinks is divided into 5 pieces ? I think they should conbimed into 2 exons according to the comparison of gene models, and it also seems ignore the junction information identified by tophat. Does anyone have some ideas
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