Question: Sfffile Program Of Roche 454
gravatar for Prisni
7.8 years ago by
Newcastle upon Tyne
Prisni10 wrote:

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?

next-gen snp sequencing • 4.0k views
ADD COMMENTlink modified 7.8 years ago by lexnederbragt1.2k • written 7.8 years ago by Prisni10
gravatar for Rcjk
7.8 years ago by
Rcjk10 wrote:

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.

ADD COMMENTlink written 7.8 years ago by Rcjk10
gravatar for lexnederbragt
7.7 years ago by
Oslo, Norway
lexnederbragt1.2k wrote:

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 = "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.

ADD COMMENTlink written 7.7 years ago by lexnederbragt1.2k
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