[aligenie]

Hi aligenie,

Since you define the name for the set of barcodes as 'barcode', which is the line above {, would the following command work?

sfffile -mcf barcode.txt -s barcode read.sff


In my case, for my own customized adapters, I use a barcode file with example in the comment lines (change the x with your barcodes):

/* User-defined MID sets for the 8 Y adapters...

An example:

sfffile -s Y -mcf Yscheme.txt -o region1 NameOfYourSFFfile1.sff > MIDyieldR1.txt
sfffile -s Y -mcf Yscheme.txt -o region2 NameOfYourSFFfile2.sff > MIDyieldR2.txt

*/
Y
{
mid = "Y3", "xxxxxxxxxx", 1, "xxxxxxxxxx";
mid = "Y5", "xxxxxxxxxx", 1, "xxxxxxxxxx";
mid = "Y8", "xxxxxxxxxx", 1, "xxxxxxxxxx";
mid = "Y9", "xxxxxxxxxx", 1, "xxxxxxxxxx";
mid = "Y10", "xxxxxxxxxx", 1, "xxxxxxxxxx";
mid = "Y11", "xxxxxxxxxx", 1, "xxxxxxxxxx";
mid = "Ya1", "xxxxxxxxxx", 1, "xxxxxxxxxx";
mid = "Ya2", "xxxxxxxxxx", 1, "xxxxxxxxxx";
}

So when I try these commands, I get ERROR: Default MID sets gsMIDs and flMIDs do not exist in configuration file. What is odd is that they do. I don't even want to use the MIDConfig.Parse file which is why I use the -mcf command so I think it is very odd. Should I put my barcode.txt file in the config folder?

[sklages]

So when I try these commands, I get ERROR: Default MID sets gsMIDs and flMIDs do not exist in configuration file. What is odd is that they do. I don't even want to use the MIDConfig.Parse file which is why I use the -mcf command so I think it is very odd. Should I put my barcode.txt file in the config folder?

With -s you tell sfffile to split default barcodes from default barcode file.
Put your barcodes as supposed into a file, and then, in your case use e.g.

sfffile -s barcode -o myNewSFF -mcf /path/to/barcodefile *.sff

cheers,
Sven

[aligenie]

With -s you tell sfffile to split default barcodes from default barcode file.
Put your barcodes as supposed into a file, and then, in your case use e.g.

sfffile -s barcode -o myNewSFF -mcf /path/to/barcodefile *.sff

cheers,
Sven

For some reason, that still doesn't work. Oh well, thanks for your help. Maybe I'll figure something out eventually. This is a bit of a mystery to me!

[zhengz]

Hi ali,

I guess the sfffile looks for the barcode set which you define in your barcode file and the name you specify in the command line after -s. If no match, it continues to look for gsMID and rlMID. Maybe you can remove the lines after gsMID or rlMID (yes, save a copy first), and see what the error message suggests you. Hope it works out for you eventually.

A side note: I think it is better to avoid using "*.sff", which will combine the samples having the same barcode but from different physically separated Regions (Lanes) in one sff file. Better to spell out the sff file name, instead of using wildcard. But if you have no sent the results to others, no worries, you will notice the problem, and it is quick to run the sfffile command again. It finishes in a minute.