User: alistairnward

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alistairnward210
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3 years, 4 months ago
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Posts by alistairnward

<prev • 14 results • page 1 of 2 • next >
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Answer: A: map methylome data with GKNO mosaik program
... As mentioned above, Mosaik is not ideal for your task. I am not familiar with processing methylome data, but you would definitely want to employ a tool that has been developed specifically for handling this type of data. Mosaik was not developed with this in mind. We would be happy to host tools to ...
written 5.3 years ago by alistairnward210
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Answer: A: jellyfish failing to install while building gkno
... Ok, thanks for this. I need to go and check on the dependency checking at the start of building gkno. I think I found that pkg-config was also a problem for Mac installations, so we weren't explicitly checking for it. I need to get these updated and then provide instructions on installing all of the ...
written 5.4 years ago by alistairnward210
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Comment: A: gkno install failing on [get] Getting: http://repo1.maven.org/maven2/org/apache/
... Did Pierre's suggestion help with this problem? ...
written 5.4 years ago by alistairnward210
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Answer: A: jellyfish failing to install while building gkno
... If you take a fresh clone of gkno and build it, what is the error log from gkno that you get from the Jellyfish failure? Jellyfish is the tool that we've had the most trouble getting to run on most systems, but seems to be running on all the systems we've tested so far. There could be some dependenc ...
written 5.4 years ago by alistairnward210
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Answer: A: The best method for analyzing mobile element insertion sites at some regions by
... One more addition to this post. I have updated the pipeline so that you can parallelise alignment of multiple fastq files and then parallelise the detection as part of the same pipeline. A brief tutorial is provided to explain how to go about doing this: http://blog.gkno.me/post/88719010295/call-me ...
written 5.4 years ago by alistairnward210
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Answer: A: The best method for analyzing mobile element insertion sites at some regions by
... I just updated the pipeline to allow specification of a list of regions. Please update to version 1.25.6. If you generate a list of regions (there are a couple of tools within gkno to help with this, e.g. gkno region-by-dict if you want to specify regions of a certain window size), then you can feed ...
written 5.4 years ago by alistairnward210
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Answer: A: gkno troubleshooting in Mac OS 10.8.5
... Hi Kizuna, We're looking into these problems at BC. Unfortunately, we haven't been able to test all of the tools on all possible operating systems, so we sometimes run into some problems. In the meantime, gkno is completely operational using all of the other tools. If you type ./gkno, you should se ...
written 5.5 years ago by alistairnward210
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Answer: A: How to get reads, which I filtrate
... You can use bamtools to perform all sorts of BAM filtering tasks. Try the software at gkno.me (click on the 'Try it' button for simple instructions on getting the software) and you can get a while resource for next-generation sequencing analysis. To get the reads with mapQ less than 10, the followin ...
written 5.5 years ago by alistairnward210
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Answer: A: What is the best programming language for NGS data analysis pipeline development
... As already mentioned, the language depends on the analysis that you are attempting to perform. There are a number of projects out there that attempt to handle provide pipelines for you. For example, see the gkno project (gkno.me) for a set of tools and pipelines. Developing pipelines can be achieved ...
written 5.5 years ago by alistairnward210
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Answer: A: NGS pipeline analyses
... Hi Kizuna, We, in Gabor Marths lab at Boston College, have an NGS tool and pipeline launcher that is simple to use and can perform a variety of different analyses with prebuilt pipelines. Customizing pipelines is straightforward and we are always available to help. Check out our site at http://gkno ...
written 5.5 years ago by alistairnward210

Latest awards to alistairnward

Teacher 5.3 years ago, created an answer with at least 3 up-votes. For A: How to get reads, which I filtrate
Scholar 5.5 years ago, created an answer that has been accepted. For A: How to get reads, which I filtrate
Teacher 5.5 years ago, created an answer with at least 3 up-votes. For A: NGS pipeline analyses
Teacher 5.5 years ago, created an answer with at least 3 up-votes. For A: NGS pipeline analyses

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