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  • #16
    Thank you.

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    • #17
      Originally posted by maubp View Post
      It 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.
      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?
      Last edited by jiltysequence; 06-23-2011, 10:20 AM.

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      • #18
        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
        )

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        • #19
          Originally posted by sunsnow86 View Post
          Is there any one know a script which can convert sanger fastQ (phred+33) to illumina fastQ( phred+64
          )
          Did you read all this thread? e.g. My earlier post said:

          Originally posted by maubp
          You can use several existing tools to do the conversion from Illumina FASTQ to Sanger FASTQ, including EMBOSS seqret, Biopython, BioPerl, BioJava, BioRuby etc.
          These tools can also do the reverse conversion.

          You can also do this in Galaxy

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          • #20
            I can't seem to get seqret to read files at all. It keeps saying Died: seqret terminated: Bad value for '-sequence' and no prompt

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            • #21
              Originally posted by Kotoro View Post
              I can't seem to get seqret to read files at all. It keeps saying Died: seqret terminated: Bad value for '-sequence' and no prompt
              It 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?

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              • #22
                Originally posted by maubp View Post
                It 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?
                I had installed with the RPMS so the version was 5.0.0

                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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                • #23
                  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.

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                  • #24
                    Originally posted by Kotoro View Post
                    I had installed with the RPMS so the version was 5.0.0
                    FASTQ 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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                    • #25
                      Originally posted by maubp View Post
                      FASTQ 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).
                      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.

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                      • #26
                        Is there a way to get seqret to leave in the labels on the + lines? Do these labels even matter?

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                        • #27
                          Originally posted by Kotoro View Post
                          Is there a way to get seqret to leave in the labels on the + lines? Do these labels even matter?
                          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 it

                          Comment


                          • #28
                            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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                            • #29
                              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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                              • #30
                                Bwa

                                Thanks Jon,

                                Actually that is true I have to do the seq variation.

                                Once again I appreciate your help.

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