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Old 04-30-2008, 04:16 PM   #1
ShaunMahony
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Default Converting FASTQ to RMAP prb files

Does anyone know what the proper conversion is between Phred quality scores and the probability values required by the RMAP alignment software? RMAP's documentation doesn't have much to say on the matter.
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Old 05-09-2008, 12:13 PM   #2
ShaunMahony
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I think I've answered my own question...
RMAP seems to be pretty fussy about the prb file format. The four probabilities at each base are given as Solexa/Phred qualities (e.g: 40 -40 -40 -40). They seem to use spaces to separate the four probabilities and tabs to separate the blocks of probabilities for each base. I don't know how necessary that is but I didn't mess with it. RMAP does seem to be sensitive to the end of the line. There cannot be whitespace at the end of the line except for the newline. Each line represents a single read, so you have 4 x readLength numbers on each line and there are no labels so they have to be in the exact same order as your corresponding FASTA file of sequences.

Of course, FASTQ quality strings only give the probability that the called base is correct. To make pseudo-probabilities for the other three bases, I have been subtracting the FASTQ probability from 1, dividing by three, and converting back into a Phred quality.

I have a script working to do the conversion in case anyone is interested.

I wish that RMAP would support FASTQ files as an option... our core facility is currently throwing out the prb files.

Last edited by ShaunMahony; 05-09-2008 at 12:16 PM.
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Old 05-13-2008, 08:47 AM   #3
RudyS
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at least some core facility support dont understand the value of the prb files ... after thinking about doing what you did, i decided it didnt make sense to try to reverse-engineer the prb scores ... note that for equivalent probabilities, the fastq file will simply select the first (!?) ... if you run the script on a fastq file that you actually have the prb file and learn something, it would be interesting to know how much "better" rmapq with the prb file does over just rmap with the fasta file ...
i think?
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