[SylvainL]

I do not understand why you took so short reads...

Which command line did you use for fastx_trimmer?

[Inma]

I used "./fastx_trimmer -t 32 -i /home/inma/Escritorio/454reads.fasta", but I'm not sure if it's correct.

[SylvainL]

Obviousély it is not!!

Why you do not use the command line I sent you last time?
This command line will extract the first 120nt of each read... (if you want the last 120nt, you can use your command line but with -t 120)

fastx_trimmer -f 1 -l 120 -i input -o output

Edena can not do miracles with 32nt_long reads.

I also already asked you but how many reads do you have (this point is crucial to know if it makes sens to use Edena...)

Cheers,

Sylvain

[Inma]

Ok SylvainL.

I have 301453 reads (454 reads). I'm going to try this command line, Thank you!

[SylvainL]

Do you have an estimation of your genome size?

[krobison]

Which assembler are you using? It may be valuable to try multiple assemblers (for 454 data Celera, MIRA & Newbler are obvious ones to try) and compare the results.

Assembling with 32 nt reads might give you the most confident regions, but otherwise it's challenging to see that gaining you much. I would also caution that the different major error mode of 454 data (indels due to homopolymers) may confound a tool such as Edena. In general, it's hard to see how converting long reads to short reads is a gain; you are throwing out a lot of valuable information.

[Inma]

Yes, I have. It's about 4,5 Mb