Hi all,
I am new to the forum, and I am working with a Illumina GA II data. I have done sequence alignment using Bowtie. My goals is to detect differentially expressed genes over two populations just like microarray analysis. Can someone recommend an easy-to-use software to perform this task?
I have tried many, and the pile-up functionality does not solve my problem. What I'd like to have is to retrieve counts for each short read with genome annotation such as gene name etc.
Thanks very much!
Questioner
I am new to the forum, and I am working with a Illumina GA II data. I have done sequence alignment using Bowtie. My goals is to detect differentially expressed genes over two populations just like microarray analysis. Can someone recommend an easy-to-use software to perform this task?
I have tried many, and the pile-up functionality does not solve my problem. What I'd like to have is to retrieve counts for each short read with genome annotation such as gene name etc.
Thanks very much!
Questioner
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