454 Raw datas

[Giancarlo]

Hello!

I am quite new with 454 sequencing and I just got my first run (raw data). The files are in this format:
C1226_SV911631_RunID28380309_reads.tgz
C1226_SV911631_RunID28380309_sff.tgz
C1226_SV911631_RunID28413700_reads.tgz
C1226_SV911631_RunID28413700_sff.tgz
C1226_SV911631_SID16663_assembly.tgz
C1226_SV911631_SID16664_assembly.tgz

I have really no idea where to start....we used an external sequencing service and this we get...Does anyone know if I need special software to open the files?
What do they mean reads.tgz, sff.tgz, and assembly.tgz?
I really need help for something that you could find very simple and stupid.
Thanks a lot!
Giancarlo

[RCJK]

Hi Giancarlo,

If you are unsure of what files your provider has given you, you should ask them to clarify what they are. I'd say they have given you the reads, the sff files, and the assembly (de novo) files for two region or two samples. The .tgz is a compressed archive (if I am getting the terminology correct), so you should be able to decompress it and more files will be present.

[Giancarlo]

Hi RCJK,

thanks for your reply. I also think I have received the reads and assembly. Yes, these are two samples, but when I decompress the files I have at the end this sff file that I am not able to open on a windows operating system. That's why I was wondering if I need some other programs for visualize the files. What I want to see is which sequences are inside...if we got what we want or not
Thanks again,
Giancarlo

[nicolallias]

From a sff you can extract (even on a Windows) fasta and quality files with sff_extract.
You may also have a look on this page this page.

[ulz_peter]

Hi Giancarlo,

You can open sff files within the Software shipped by Roche (which unfortunately only runs in Linux). However, you should be able to open the reads files (usually in Fastq format which you should be able to open using a text editor like Notepad in windows). The only problem could be the size of the files...
For the assembly files there are several possible format although the Roche software only outputs .ace files. These are text-based as well and also very large. If you do not possess a 64bit Windows system this could be a problem...

If you want to visualize the assembly you could go with Tablet:
Link: http://bioinf.scri.ac.uk/tablet/

it can handle .ace files and runs in windows.

I hope this helps...
(Nevertheless, when dealing with NGS data I would suggest changing to Linux as most bioinformatic analysis programs work well in Linux but not in Windows...)

Could you describe the experiment in more detail (which organism, de-novo sequencing, resequencing, targetted sequencing,...). This has a great influence on the choice of analysis software.

[Giancarlo]

hi guys,

thanks for the suggestions. I will check carefully all of these otpions and I will let you know (or I will ask Roche to ship me the software, should be not a problem). Yes, the files are quite big, but I'll try anyway. To be short this is a transcriptome sequencing of a tumor cell line. If you know good and more specific software for RNAseq would be nice to know which one you find best.
All the best,
Giancarlo

[joscarhuguet]

hi guys,

thanks for the suggestions. I will check carefully all of these otpions and I will let you know (or I will ask Roche to ship me the software, should be not a problem). Yes, the files are quite big, but I'll try anyway. To be short this is a transcriptome sequencing of a tumor cell line. If you know good and more specific software for RNAseq would be nice to know which one you find best.
All the best,
Giancarlo

You could extract fasta and quality files from the sff files. Then you could use MIRA assembler. The information here.

http://sourceforge.net/apps/mediawiki/mira-assembler/index.php?title=Main_Page