Does anybody have a tested program to convert Illumina CASAVA 1.8 qual scores (Phred+33) to the previous version Illumina 1.5+ (Phred+64)?
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What about something that I can run in the command lene?
Most programs should work with Phred+33 (e.g. append '-Q 33' to the fastx command line).
Also, Biopython can read files as one format and write them as another:
Here's a quick python conversion script, derived from an example on that page:
Code:#!/usr/bin/python from Bio import SeqIO SeqIO.convert("input.fastq", "fastq-sanger", "output.fastq", "fastq-illumina")
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Originally posted by gringer View PostWhy do you need a Phred+64 offset and/or the command line?
Originally posted by gringer View PostMost programs should work with Phred+33 (e.g. append '-Q 33' to the fastx command line).
Also, Biopython can read files as one format and write them as another:
Here's a quick python conversion script, derived from an example on that page:
Code:#!/usr/bin/python from Bio import SeqIO SeqIO.convert("input.fastq", "fastq-sanger", "output.fastq", "fastq-illumina")
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Originally posted by lpn View PostBecause tophat doesn't seem to handle well Phred+33 (CASAVA 1.8), but works with Phred+64 (CASAVA 1.5+).
There's also the Bowtie "--phred33-quals" option, which I guess you could add to tophat's bowtie call to force this:
Code:nano $(which tophat)
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As gringer said if you DO NOT specify a qual flag it will work fine. You are not the only person with HiSeq data which finally encodes the quality values in the standard sanger format for which nearly all programs expect by by default. The flag, for most today, is just for processing legacy datasets.
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Originally posted by gringer View PostThis is interesting and doesn't match my experience with tophat on recent Illumina runs. Do you have any "--solexa1.3-quals" options on your command line? Removing that should stop bowtie from using Phred+64, and go back to the default Phred+33.
There's also the Bowtie "--phred33-quals" option, which I guess you could add to tophat's bowtie call to force this:
Code:nano $(which tophat)
Last edited by lpn; 03-03-2012, 07:53 AM.
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Originally posted by lpn View PostThat works, but subsequent analysis produces strange results.Last edited by gringer; 03-03-2012, 11:57 AM.
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