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Originally posted by maubp View PostIt will depend on which Galaxy installation you are using (e.g. the main http://usegalaxy.org Penn State one), and how busy it is with other people's work. If you asked on the Galaxy mailing list you'd probably get a better answer.Last edited by jiltysequence; 06-23-2011, 10:20 AM.
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Originally posted by sunsnow86 View PostIs there any one know a script which can convert sanger fastQ (phred+33) to illumina fastQ( phred+64
)
Originally posted by maubpYou can use several existing tools to do the conversion from Illumina FASTQ to Sanger FASTQ, including EMBOSS seqret, Biopython, BioPerl, BioJava, BioRuby etc.
You can also do this in Galaxy
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Originally posted by Kotoro View PostI can't seem to get seqret to read files at all. It keeps saying Died: seqret terminated: Bad value for '-sequence' and no prompt
Also, what version of EMBOSS do you have - what does the embossversion command give?
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Originally posted by maubp View PostIt would help if you showed us the example command that failed and the exact error message.
Also, what version of EMBOSS do you have - what does the embossversion command give?
it doesn't seem to balk being given fastq-illumina as a format specifier, while it does copmlain about just fastq.
seqret fastq-illumina::test.fq fastq-sanger::stdout
Reads and writes (returns) sequences
Error: Unable to read sequence 'fastq-illumina::test.fq'
Died: seqret terminated: Bad value for '-sequence' and no prompt
just to show:
seqret fastq::test.fq fastq::stdout
Reads and writes (returns) sequences
Error: Unknown input format 'fastq'
Error: Unable to read sequence 'fastq::test.fq'
Died: seqret terminated: Bad value for '-sequence' and no prompt
I'm trying to build the newest version from source now, and I'll see if it works.
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Originally posted by Kotoro View PostI had installed with the RPMS so the version was 5.0.0
As to up to date RPMS, recent EMBOSS releases seem to exist on https://admin.fedoraproject.org/updates/ (search for EMBOSS in upper case).
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Originally posted by maubp View PostFASTQ support was added in EMBOSS 6.1.0 patch 1, so that was the problem.
As to up to date RPMS, recent EMBOSS releases seem to exist on https://admin.fedoraproject.org/updates/ (search for EMBOSS in upper case).
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BWA with sanger FASTq file
I have Fastq files with Sanger quality score and I want to align to human genome using BWA. The question is if I dont use -I then will it work or I need to make some more changes so that it can work with Sanger quality score. In the BWA manual it is mentioned that use -I option for illumina FASTq fastq.
I apologise for my poor programing knowledge
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If you have fastq files from a HiSeq run it most likely is sanger format fastq not the old illumina format that requied the -I option. So just run bwa without the -I option and you should be fine.
FYI - BWA alignment doesn't actually care about the quality encoding, but doing it properly is needed if you want to do variant calling.
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