Help getting started

[viralnerd]

Hello everyone,

I am just getting started analyzing some 454 data, and I have downloaded a bunch of tools. Can you please offer some advice for newcomer to the field who is just getting started. Here are the things that I want to be able to do:

1. Determine the quality of the sequence run: Is there any program that will give an overview of the quality of the reads in an .sff file?

2. Clip adapter sequences that might be there from a titanium 454 run and bin the large file into 10 smaller ones by barcode.

3. Clip the barcodes.

4. Assemble contigs.

I am working with a very complex sample and it looks like I am getting a lot of small contigs that are really divergent from any known reference sequences. Can anyone offer advice on assembly difficult sequences!

Thank you,

viralnerd

[maubp]

I would start by trying to get the Roche Newbler software (Linux only),

http://seqanswers.com/forums/showthread.php?t=114

[viralnerd]

I have tried Newbler...

Thank you for the post.

I have tried Newbler through our campus network and have found it to be very slow and cumbersome. In fact, it never returned any assembly whereas other programs like Geneious and CodonCode Aligner built nice contigs...

I know that it is probably my inexperience with Newbler... does anyone know of a tutorial for this tool or others?

Thanks everyone, I really appreciate the help getting started in this exciting work. Since my data came in, I have hardly slept!

[maubp]

Newbler has both a command line interface (which I use) and a GUI. Which did you try?

When you say you ran it through the network, were you using X-Windows or something? i.e. Was all the file access and computation being done on the server?

Anyway, read the manual on the command line tools sffinfo and sffile - these will take care of the barcode stuff for you.

[viralnerd]

Continuing discussion of Newbler

Yes, I tried the GUI version using X11. The computation was done on the university computer. I prefer the command line and will see if I can access that. I will take a look at the manual focusing on the topics you recommended.

Thanks for your help.

viralnerd