Sfffile Program Of Roche 454
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11.0 years ago
Prisni ▴ 10

hi there!!

I need to remove mids and mid sort my sff files while retaining its sff format.

I intend to used SWAP454 for SNP calling in my sff file.

I am unable to find a proper way of doing s using sfffile program over command line.

sfffile -o roche454_trimmed.sff -e mid.lst -nmft sff/roche454.sff

mid.lst is my MID file is GSMID format.

roche454.sff is my sff file that I need should be trimmed off at MIDs.

Can anyone please suggest?

snp next-gen sequencing • 4.7k views
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11.0 years ago
Rcjk ▴ 10

If I understand what you are trying to do, I think you'll need to create your custom MIDConfig.parse (modify the existing one and save as a new name) file and then try this:

sfffile -s GSMID roche454_trimmed.sff -mcf /locationof/customMIDConfig.parse sff/roche454.sff

This would sort your "roche454.sff" into separate files by GSMID located in "customMIDConfig.parse" (or whatever you wanted to call it.

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11.0 years ago
lexnederbragt ★ 1.3k

You write that the mid.lst file is in GSMID format. Then you should use the -mcf flag instead of the -e flag. Also, please make sure the file adheres to the following structure:

mid_set_name
{
     mid = "name1", "ACGT", 1;
     mid = "name2", "CGTA", 1;
     mid = "name3", "GTAC", 1;
}

The number at the end is the maximum number of allowed errors in the MID sequence.

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