Not yet, but I am about to subject some samples to Helicos sequencing.
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Originally posted by nekrut View PostWe have not see the data ourselves yet, but I just asked Helicos guys to send us a few files. Do you have any to share?
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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.
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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 PostHi, upload limitations are going to be a problem for all of us as it is not Galaxy issue per se. To upload your files try this:
- gzip them
- put them to a web-accessible loocation
- paste a URL pointing to your files to upload tool as shown in the attached image
Aspera is incredibly expensive to license, and we're not convinced it really accelerates things that much. There are some open source alternative we will be taking a look at
Yes, blasting against custom db is on the to do list as numerous people want this to happen.
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Originally posted by brian.g View PostUDT (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.
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