Hi,
I have Hi-seq directional paired-end data. I used the standard pipeline based on their "Nature protocol" paper to assembly and compare the annotated genes. It is very strange that cufflinks did not assembly a highly-expressed mark gene (which is well-known in my cell-type)
. Have anyone else also met the similar problem of cufflinks previously? Is that the bug of cufflinks or the problem of processing with cufflinks / parameters?
Many thanks!
I have Hi-seq directional paired-end data. I used the standard pipeline based on their "Nature protocol" paper to assembly and compare the annotated genes. It is very strange that cufflinks did not assembly a highly-expressed mark gene (which is well-known in my cell-type)
![Confused](https://www.seqanswers.com/core/images/smilies/confused.png)
Many thanks!
![Smile](https://www.seqanswers.com/core/images/smilies/smile.png)
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