random downloading of .sff file

[paa6]

I already have .sff file but I guess that is corrupted but still I want to check that whether my software is able to import .sff file or not....

I am working on geneious software. So, I have tried a lot to download any random file in .sff format so that I can try to import in geneious but I didn't get it from anywhere.

[TiborNagy]

I guess you would like to download example SFF files. The IonCommunity has some test data for IonTorrent.

[paa6]

I guess you would like to download example SFF files. The IonCommunity has some test data for IonTorrent.

I did try in this community but sadly I didn't get any kind of .sff file...

[TiborNagy]

Two years ago I had downloaded SFF files from the community. It was a part of a grand challange.

[paa6]

Two years ago I had downloaded SFF files from the community. It was a part of a grand challange.

ohh can u attach any random .sff file if possible...

[GenoMax]

You should be able to find SFF files on NCBI-SRA. http://www.ncbi.nlm.nih.gov/sra They will be in SRA format (search for 454 datasets). You will then have to convert them into SFF.

[sklages]

I already have .sff file but I guess that is corrupted but still I want to check that whether my software is able to import .sff file or not....

I am working on geneious software. So, I have tried a lot to download any random file in .sff format so that I can try to import in geneious but I didn't get it from anywhere.

For the general ability to read SFF files you should ask the support team of your software and/or look at their website and have a look at the manual.

To check if your SFF file is corrupt you can either

a) use 'strings' and see if the file ends with readnames
b) use sffinfo from the Roche SFF Tools to see, if the file can be read/parsed. If not, you'll get an error and you can be sure that your file is corrupted (as the SFF Tools are definitely able to read SFF files :-) )

hth

[harlequin]

I already have .sff file but I guess that is corrupted but still I want to check that whether my software is able to import .sff file or not....

I am working on geneious software. So, I have tried a lot to download any random file in .sff format so that I can try to import in geneious but I didn't get it from anywhere.

Hi,

In case you don't mind them being generated by a simulation software, I've recently uploaded many 454Sim-generated SFFs under http://www.ibi.vu.nl/downloads/, see the section 454 data used in and the corresponding readme file.

Cheers

[paa6]

You should be able to find SFF files on NCBI-SRA. http://www.ncbi.nlm.nih.gov/sra They will be in SRA format (search for 454 datasets). You will then have to convert them into SFF.

I did try that but I couldnt found..ok I will try again...

[paa6]

For the general ability to read SFF files you should ask the support team of your software and/or look at their website and have a look at the manual.

To check if your SFF file is corrupt you can either

a) use 'strings' and see if the file ends with readnames
b) use sffinfo from the Roche SFF Tools to see, if the file can be read/parsed. If not, you'll get an error and you can be sure that your file is corrupted (as the SFF Tools are definitely able to read SFF files :-) )

hth

thanks a lot...I will try this...

[paa6]

Hi,

In case you don't mind them being generated by a simulation software, I've recently uploaded many 454Sim-generated SFFs under http://www.ibi.vu.nl/downloads/, see the section 454 data used in and the corresponding readme file.

Cheers

thanks a lot....but the thing is that I tried this link but other sites r getting opened on the same page...

[GenoMax]

thanks a lot....but the thing is that I tried this link but other sites r getting opened on the same page...

See the README: http://www.ibi.vu.nl/downloads/454CO...rchives.README

Download one of the files (> 2G file) : http://www.ibi.vu.nl/downloads/CORE_1.tar.gz

[GenoMax]

I did try that but I couldnt found..ok I will try again...

Here is an example SFF file: http://www.ncbi.nlm.nih.gov/sra?term...0cluster_dbgap (click on the "size" to download).

As I said before this particular file will be in .sra format (which is a special format that SRA uses). You will have to use sff-dump program found in the SRA-toolkit: http://www.ncbi.nlm.nih.gov/Traces/s...?view=software to convert the .sra file to the original SFF format.

[paa6]

Here is an example SFF file: http://www.ncbi.nlm.nih.gov/sra?term...0cluster_dbgap (click on the "size" to download).

As I said before this particular file will be in .sra format (which is a special format that SRA uses). You will have to use sff-dump program found in the SRA-toolkit: http://www.ncbi.nlm.nih.gov/Traces/s...?view=software to convert the .sra file to the original SFF format.

THANK U SO MUCH i WILL TRY THAT...

[sklages]

.. still wondering why you don't have a look at the manual and/or ask geneious support team ..