something about my 454 result

[oyjenvol]

HELLO Tangsha
can you leave a communication way to me? I want to ask you some questions about 454 sequencing. now i am in ,Sun yat-sen university,Guangzhou .

my QQ:409517906
Email: [email protected]

[sklages]

You will *need* SFF files if you submit your data to NCBI (e.g. for publication isues)

[nickloman]

You want the SFF files, ideally.

[tangsha1986]

Really sorry to bother you rglover, but thanks a lot for your help
I will take your words next time.

[rglover]

Hi,

You'll have to contact the sequencing company if they haven't included the quality files in with your sequences. You'll only get quality files which match the reads inside the .fna files - you won't get quality files for the contigs.

As a polite request, could you not send PMs if people haven't replied to your thread in a matter of hours? I check the forum at least once a day but I'm not here constantly - it's a little annoying to get a PM that essentially says "please respond to my thread".

[tangsha1986]

thank you

thank you I have reply in my thread
please have a look

[tangsha1986]

Thank you rglover and Adams
I have unzip the 4 files above,I got
2.TCA.454Reads.fna
1.TCA.454Reads.fna
stress454AllContigs.fna
stress454AllContigs.fna
But I found no qual files. So what do you think about the files? Are there any other files I need?

[ian Adams]

yes I would expect that you have your raw reads in the files "Stressed_454Reads.zip" and "Control_454Reads.zip" probably as .fna and .qual
The .fna file is the sequences in .fasta format and the .qual file will contain the quality valves for each base. These files should be significantly bigger than the others. The "allcontig" files will contain contigs produced from your reads using the 454 Newbler software.
Good luck

[rglover]

Hi,

I suspect that you'll find either a .sff or your .fna and .qual files if you unzip the .zip files. WinRar (www.rar-lab.com) is pretty good, but if you're using Windows you should just be able to double click the files and Windows will extract them for you.

Cheers,
Rachel

[tangsha1986]

May some experienced people tell me what other files I should ask the company for to do the later detailed analysis? I am a newly learner in this filed.

[tangsha1986]

Hello everyone：）
I have just finish a 454 transcriptome sequencing by FLX-Ti
The company send me 6 result files：
454BaseCallerMetrics.txt
454NewblerMetrics.txt
Stressed_454Reads.zip
Stressed_454AllContigs.zip
Control_454Reads.zip
Control_454AllContigs.zip
I wonder if these are complete results. Because I see some paper say some
SFF files and .qual.
Shall I ask the company to send me more files? For example? someone help me ,thank you