Starting cancer transcriptome analysis of 454 sequencing data

[ketan_bnf]

Hi all,

We have a cancer related transcriptome data which is sequenced using 454 GS-FLX titanium, for which reference genome is available.

I want to set work pipeline for bioinformatics analysis, so I need help regarding from where to start, which software to use and best for 454 long read data as i am going to perform gene expression analysis. Linux operating is no issue for software, as i am working on both windows & linux. So far i have tried CLC genomics workbench and DNASTAR's QSeq.

Looking forward for useful inputs/suggestions.

Thanks.

[Strand SI]

You are welcome to try Avadis NGS for your analysis.

Disclaimer: we are the developers, but felt it was fair to suggest it in light of the other tools you said you tried.