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Thank you.
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Has the Galaxy server ever been known to go down? I am having some trouble accessing the download at the moment. No errors just too long of a wait that I am giving in. Thirty minutes is too long when you are on a deadline. I have been running some simulations to test different compositions of structural foams and plastics. I have been considering using them in a scientific construction class for university. Now I just need to find out who else is into manufacturing these products. Have you guys ever heard of www.dekalbplastics.com?Originally posted by maubp View PostLast edited by jiltysequence; 06-23-2011, 10:20 AM.Comment
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conver sanger fastQ into illumina fastQ
Is there any one know a script which can convert sanger fastQ (phred+33) to illumina fastQ( phred+64
)Comment
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Did you read all this thread? e.g. My earlier post said:Originally posted by sunsnow86 View Post
These tools can also do the reverse conversion.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 GalaxyComment
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I can't seem to get seqret to read files at all. It keeps saying Died: seqret terminated: Bad value for '-sequence' and no promptComment
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It would help if you showed us the example command that failed and the exact error message.Originally posted by Kotoro View Post
Also, what version of EMBOSS do you have - what does the embossversion command give?Comment
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I had installed with the RPMS so the version was 5.0.0Originally posted by maubp View Post
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.Comment
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seems to work fine, someone should get around to making RPM of the new versions for red hat systems.
I would if I knew how to make packages.Last edited by Kotoro; 06-21-2011, 02:31 PM.Comment
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FASTQ support was added in EMBOSS 6.1.0 patch 1, so that was the problem.Originally posted by Kotoro View Post
As to up to date RPMS, recent EMBOSS releases seem to exist on https://admin.fedoraproject.org/updates/ (search for EMBOSS in upper case).Comment
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Seems that there are some, unfortunately I'm using RHEL 6.1, and I should be using EPEL6 packages. It doesn't appear that there are any.Originally posted by maubp View PostComment
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Is there a way to get seqret to leave in the labels on the + lines? Do these labels even matter?Comment
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No, they are deliberately left out to save disk space. This shouldn't matter - and if you find a tool that doesn't like it, ask them to fix itOriginally posted by Kotoro View Post
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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 knowledgeComment
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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.Comment
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Bwa
Thanks Jon,
Actually that is true I have to do the seq variation.
Once again I appreciate your help.Comment
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
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