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Not yet, but I am about to subject some samples to Helicos sequencing.
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I do not know about the raw output from the Heliscope, but what i have seen was fasta format for the reads and BED format for the alignments. Some Helicos datasets are available there: http://open.helicosbio.com/mwiki/index.php/Datasets (a free registration is maybe required though). Actually, Helicos RNA-seq data can also be obtained from the UCSC Table Browser and sent to Galaxy, or from the UCSC ftp download page.Originally posted by nekrut View PostComment
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Problem with Helicos is that it doesn't come as FASTQ (quality scores are assigned to reads, not nucleotides within the reads). The best (only?) way to handle this is to convert the original format to FASTA after filtering at a given quality cutoff and take it from there. There are also tools to create 'fake' FASTQ files by setting the quality score to a uniform value if a tool absolutely requires FASTQ.
You almost need to use their filtering workflow anyway as it gets rid of a number of artifacts which are otherwise difficult to remove.Comment
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UDT (udt.sf.net) should work. It is a library with C++/JNI/.net API and only has a simple command line tool. You can also look at HSCP (http://sourceforge.net/projects/hscp/), which is a SCP-like tool but uses UDT for data transfer. Both UDT and HSCP are open source and free to use.
Originally posted by nekrut View PostComment
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I have been playing with Galaxy on my local machine for the past few days. It is great piece of software, and was relatively easy to plug in new tools. Thank-you again.Comment
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Nils:
Thanks for sending us your wrappers. They will be on public site shortly!Comment
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If there is anything the site or community can do to support this effort, don't hesitateComment
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I think it is important to include bfast as perm/bowtie do not do gapped alignment.Comment
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