[GenoMax]

Did you replace "filename.sff" with the real file name when you ran the command? Or is your file actually named "filename.sff"?

$ strings your_actual_file_name.sff | grep run_type

Can you post the size of the SFF file?

$ ls -lh your_actual_file_name.sff

[paa6]

Did you replace "filename.sff" with the real file name when you ran the command? Or is your file actually named "filename.sff"?

$ strings your_actual_file_name.sff | grep run_type

Can you post the size of the SFF file?

$ ls -lh your_actual_file_name.sff

yeah I typed my real file name in the place of filename, and size of the file is 607.1 mb

[paa6]

yeah I typed my real file name in the place of filename, and size of the file is 607.1 mb

I am getting this thing after typing ur commands...

[GenoMax]

So the size looks decent for a SFF file (recollecting from distant past, have not dealt with 454 data for a long while).

Do we have any additional information beyond where we left things off last night?

I have not used this program before but it seems to be able to use SFF files. Do you want to see if your file will work with this: http://www.dnabaser.com/download/SFF%20tools/

[paa6]

I am getting this thing after typing ur commands...

this is the thing i am getting...attachment in screenshot

[paa6]

So the size looks decent for a SFF file (recollecting from distant past, have not dealt with 454 data for a long while).

Do we have any additional information beyond where we left things off last night?

I have not used this program before but it seems to be able to use SFF files. Do you want to see if your file will work with this: http://www.dnabaser.com/download/SFF%20tools/

last night I have tried sff workbench too...but sadly my .sff file was not imported..dont know why?? it was showing error...infact sff workbench is pretty easy..

[GenoMax]

If that is the case then there is a distinct possibility that your SFF file is corrupt. Is there any chance that you can go back to whoever generated the data and ask for a fresh copy?

[GenoMax]

BTW: Can you edit the title of this thread (and keywords if you had put in any) in the first post? This thread is not related to illumina sequencing and it will show up in future searches.

[paa6]

If that is the case then there is a distinct possibility that your SFF file is corrupt. Is there any chance that you can go back to whoever generated the data and ask for a fresh copy?

hoe so...I am waiting for PI an dI will discuss with him...hope so that he will understand everything...ok I will try to change the title...

[GenoMax]

hoe so...I am waiting for PI an dI will discuss with him...hope so that he will understand everything...ok I will try to change the title...

You will have to choose "edit" and then "Go Advanced" to be able to edit the title.

[paa6]

I did change it...and will let u know what is he saying...still waiting for him...

[paa6]

hoe so...I am waiting for PI an dI will discuss with him...hope so that he will understand everything...ok I will try to change the title...

HEY i DID talk to him and luckily he understood...thanks a ton...

[paa6]

HEY i DID talk to him and luckily he understood...thanks a ton...

i HAVE ONE MORE que. geneious doesn't support .sff file format...

[sklages]

Well, you have a SFF file with a missing manifest. Probably corrupted.

Again, ask your PI for the "complete" dataset. There went probably something wrong during transfer. For the SFF file check the MD5 sum before and after copy process, just to be sure, that it has been transferred completely.

And, yes, it seems that geneious does not support native SFF import :-(
But if you have the complete dataset you can just use use the fna/qual pair (always use the quality files if available), just as intented from the very beginning :-)

But of course, you can have a look at "sff_extract" or Roche's "SFF Tools" just to be able to deal with SFF files on the command line.

regards.

[paa6]

Well, you have a SFF file with a missing manifest. Probably corrupted.

Again, ask your PI for the "complete" dataset. There went probably something wrong during transfer. For the SFF file check the MD5 sum before and after copy process, just to be sure, that it has been transferred completely.

And, yes, it seems that geneious does not support native SFF import :-(
But if you have the complete dataset you can just use use the fna/qual pair (always use the quality files if available), just as intented from the very beginning :-)

But of course, you can have a look at "sff_extract" or Roche's "SFF Tools" just to be able to deal with SFF files on the command line.

regards.

hmm ok thanks, I will try that..