CLC for sequence capture 454 data

[litali]

I wanted to know what is the best wat to import the reference chromosome into CLC to analyze sequence capture experiment. The sequence capture probes were built based on build 36 human genome. I have the fasta file of the desired chromosome, but then it is without annotation. I also have a gff file of the locations of the probes on the chromosome, and of course I have the 454 sequencing result files. I want to receive as much information as possible, in what genes the mutation, exons, SNPs etc. What should I use as a reference to include all those annotations?

[NextGenSeq]

You have to annotate the reference sequence yourself. There's a plug-in and pdf guide on how to do this from CLC. I posted the guide on another thread.