[nsl]

Thank you.

[jiltysequence]

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?

[sunsnow86]

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
)

[maubp]

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:

You can use several existing tools to do the conversion from Illumina FASTQ to Sanger FASTQ, including EMBOSS seqret, Biopython, BioPerl, BioJava, BioRuby etc.
http://dx.doi.org/10.1093/nar/gkp1137

These tools can also do the reverse conversion.

You can also do this in Galaxy

[Kotoro]

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

[maubp]

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?

[Kotoro]

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.

[Kotoro]

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.

[maubp]

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).

[Kotoro]

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.

[Kotoro]

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

[maubp]

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

[mathew]

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

[Jon_Keats]

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.

[mathew]

Bwa

Thanks Jon,

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

Once again I appreciate your help.