Hey everyone,
I am working on assembling a new reptile genome. I will have some pretty high coverage mRNA-seq data as well. Are there any standard gene prediction techniques that utilize both mRNA-seq data and genome sequence level data to predict genes? I found a program called Conrad that looks like it could do this kind of thing utilizing a conditional random field, but it doesn't look like it has been widely used, or maintained since 2009.
Would the best option be to use separate programs to call genes using genome sequence information, and then again using the mRNA-seq information (cufflinks or something like that maybe?), and then I could go back and somehow merge the output form the two techniques? Are there any standard methods of performing this kind of merging?
Gene annotation is another thing I will want to do with the output. I am going to hand annotate a few genes, but it would be useful if there was some kind of program that does a blast similarity based annotation with the remainder of genes.
Thank you for your suggestions!
-John
I am working on assembling a new reptile genome. I will have some pretty high coverage mRNA-seq data as well. Are there any standard gene prediction techniques that utilize both mRNA-seq data and genome sequence level data to predict genes? I found a program called Conrad that looks like it could do this kind of thing utilizing a conditional random field, but it doesn't look like it has been widely used, or maintained since 2009.
Would the best option be to use separate programs to call genes using genome sequence information, and then again using the mRNA-seq information (cufflinks or something like that maybe?), and then I could go back and somehow merge the output form the two techniques? Are there any standard methods of performing this kind of merging?
Gene annotation is another thing I will want to do with the output. I am going to hand annotate a few genes, but it would be useful if there was some kind of program that does a blast similarity based annotation with the remainder of genes.
Thank you for your suggestions!
-John
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