LAST/Poretools - where to start?
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5.6 years ago
omer.k ▴ 70

I have a bunch of fast5 file as well as a refernce genome. I'm running a Win 7 Enterprise OS.

I'd like to install and run both Poretools (https://poretools.readthedocs.io/en/latest/) and LAST (http://last.cbrc.jp/doc/last.html).

Embarrassing enough, I have no idea why neither works for me.

For Poretools, I followed the installation instructions. Then I followed the usage examples, but got errors. For example, extracting sequences in FASTQ format from a set of FAST5 file, by typing

poretools fastq test_data/*.fast5


Yields

Error: unexpected symbol in "poretools fastq"


Moving to LAST, I am not sure if this can be run in Windows OS. Can someone answer this for me? Am I supposed to run the scripts from the command line (DOS), from a compiler of some sort? I followed the instructions I downloaded Cygwin, thinking the commands had to be run in UNIX, but had no success there too.

Truly appreciate some help to get me going here.

sequencing alignment next-gen • 2.0k views
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Not the answer you ask for but the answer you need: if possible, work on linux. It will make things with tools like this so much easier.

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Yes, thank you WouterDeCoster. Luckily I've received some help from a very nice friend from a neighboring lab with some experience in sequencing. We've installed VirtualBox and than the latest Ubuntu x64. Than we've installed many packages needed for PoreTools and BWA-Mem. There were some hurdles which I could not overtake on my own (since I know nothing about UNIX), but again the friend assisted through it.

We than used a few straight forward commands and produced a sorted BAM file from the Lambda 2D control experiment. I than visualized it aligned against the Lambda phage genome using IGV (I'd appreciate suggestions for a different viewer, if you think there are more superior viewers).

To sum it up, not surprising, incompatibility of many of these alignment tools with Windows OS was setting me back. And I was obviously unaware of this bit of common yet critical knowledge, trying to figure out how to run these tools in Windows OS.

I hope this thread could serve others at the beginning of their bioinformatics learning curve..

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A VirtualBox is indeed a nice solution (but obviously you are limited in RAM used for your virtual machine). Good that you got this fixed! Getting experience with Linux and new tools can be tough first, but will definitely pay off in the long run. It's convenient that you have someone in your environment who can help you get started.

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This is very much true, the RAM restriction could be bothersome. I'm considering using a dedicated Mac for this reason.

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I'll consider this, thank you.

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I am sorry to wake this old thread up.. I'd like to install and run Poretools on windows OS nonetheless (for different reasons).

Could you please guide me? I think I've followed the instructions well. I run

conda install seaborn


In regular command line (windows). which successfully downloaded and installed/updated the following

• conda 4.4.10-py25_0
• conda-env 2.6.0-h36134e3_1
• pycosat 0.6.3-py35h456c199_0
• seaborn 0.8.1-py35hc73483e_0

Yet I am not sure in which command line/terminal am I suppose to type commands such as

poretools fastq test_data/


Am I note supposed to run the poretools.exe with the aforementioned command?

poretools.exe fastq test_data/


Thank you.

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5.6 years ago
buchfink ▴ 240

You can try diamond (https://github.com/bbuchfink/diamond), it's a protein aligner similar to LAST but it has a native Windows version that does not require cygwin.

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Thank you, I'll have a look at it.