why cufflinks can not assembly the reads mapped to genome

[rboettcher]

Is this gene included in the GTF file you provide to cufflinks? If not: did you enable the search for novel genes (--GTF-guide)?

[11xinqi]

Do those reads also match another place in the genome? I.e. they are not unique.

They dont. BC I only chose the reads that can map to genome uniquely.

[kbradnam]

Do those reads also match another place in the genome? I.e. they are not unique.

[11xinqi]

Hi, all

I want to search a specific gene from the gtf file from the result of cufflinks. But I can not find it which means there is no assembly result from cufflinks. However, I find about 240 reads can be blasted to this gene which I got from NCBI so that I know there are 240 reads can mapped to this region of genome corresponding to that gene. the blast result is shown in the picture.


My question is why cufflinks does not assembly these reads even though they are mapped to genome?