Hello all,
I work with Bioinformatics in a lab and our group received the task of mounting a plant transcriptome using sequences from 454.
We still don't have the genome sequenced so we are now defining our strategies for this project.
The first problem is related with the assembly of the sequences.
We used Newbler and Mira for the assembly and now we are lacking of metrics to compare this 2 softwares in order to decide which one is better and why.
After the assembly I think the next obvious thing to do is to align this transcriptome with the genome of arabdopsis and may be use this to decide which assembly was better and why.
Another question would be about which aligner we should use for this.
Does anyone have a suggestion or any experience to share about this project?
Thanks for help.
I work with Bioinformatics in a lab and our group received the task of mounting a plant transcriptome using sequences from 454.
We still don't have the genome sequenced so we are now defining our strategies for this project.
The first problem is related with the assembly of the sequences.
We used Newbler and Mira for the assembly and now we are lacking of metrics to compare this 2 softwares in order to decide which one is better and why.
After the assembly I think the next obvious thing to do is to align this transcriptome with the genome of arabdopsis and may be use this to decide which assembly was better and why.
Another question would be about which aligner we should use for this.
Does anyone have a suggestion or any experience to share about this project?
Thanks for help.
Comment