Question: Sfffile Program Of Roche 454
1
gravatar for Prisni
7.6 years ago by
Prisni10
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 • 3.9k views
ADD COMMENTlink modified 7.6 years ago by lexnederbragt1.2k • written 7.6 years ago by Prisni10
1
gravatar for Rcjk
7.6 years ago by
Rcjk10
Sydney
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 7.6 years ago by Rcjk10
1
gravatar for lexnederbragt
7.6 years ago by
lexnederbragt1.2k
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_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.

ADD COMMENTlink written 7.6 years ago by lexnederbragt1.2k
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