Hello All,
I'm starting my downstream analysis with my Illumina transcriptome data. I assembled the data using three diferent assemblers (CLC, Trinity and IDBA-trans), and now I'm searching for some options to identify the CDS in my transcripts. I have some questions concerning this:
1) Is there a well-described pipeline about this into the literature? I'm trying to use TransDecoder to find my CDS, but beside this I didn't heard or read anything about other programs to perform this kind of analysis (off course one can use an ORF finder program, selected the longest ORF manually and do some similarity searches to add some evidences to the real ORF).
2) Someone already tried to use augustus to predict the CDS in the transcriptomic data (without relies on a reference)? I think the main problem with transcripts and these gene prediction is the number of CDS. Each transcript must have just one CDS, and how augustus work with this? Is there any reliable result?
Thanks in advance for the help,
André
I'm starting my downstream analysis with my Illumina transcriptome data. I assembled the data using three diferent assemblers (CLC, Trinity and IDBA-trans), and now I'm searching for some options to identify the CDS in my transcripts. I have some questions concerning this:
1) Is there a well-described pipeline about this into the literature? I'm trying to use TransDecoder to find my CDS, but beside this I didn't heard or read anything about other programs to perform this kind of analysis (off course one can use an ORF finder program, selected the longest ORF manually and do some similarity searches to add some evidences to the real ORF).
2) Someone already tried to use augustus to predict the CDS in the transcriptomic data (without relies on a reference)? I think the main problem with transcripts and these gene prediction is the number of CDS. Each transcript must have just one CDS, and how augustus work with this? Is there any reliable result?
Thanks in advance for the help,
André