yes i know, but this tool does not work in my pc (he asks the java installation to make it work despite the java was instaled but the problem is still), so I want a free software with this tool that works without connection i have a software Sequencher 5.4.5 but the validity of the trial was ended
quality read software
4 answers
FaatQC does not need an Internet connection to work. You only need it to get the program
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Antonio R. Franco
There are two flavors of Java, 32 and 64 bits Check if you have installed the 64bit version
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Antonio R. Franco
Try to give a clue about the problem. You need to provide some messages given by the program when you try to execute it
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If using Windows, notice that a cmd window is opened. Within this window, you get verbose information about what is happening
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So do you want fastqc? A tool that has fastqc embedded in it? Or an alternative to fastqc?
It also depends what functionality you want from fastqc, alternatives to fastqc would be:
1) prinseq-lite: http://prinseq.sourceforge.net/manual.html#STANDALONE 2) fastx-toolkit: http://hannonlab.cshl.edu/fastx_toolkit/ 3) condetri: https://github.com/linneas/condetri 4) sickle: https://github.com/ucdavis-bioinformatics/sickle
So do you have fastqc downloaded on to your machine - you'll need to unzip FastQC v0.11.5 (Win/Linux zip file) from http://www.bioinformatics.babraham.ac.uk/projects/download.html somewhere onto your computer.
Then inside that folder, Simply double click on the run_fastqc bat file.
Does that work? If not, what it does it say.
I think there is an issue with Kaspersky blocking execution of .bat files - so is blocking the run_fastqc bat file: http://superuser.com/questions/400291/kaspersky-is-blocking-my-batch-file
Essentially, all that file contains is this:
java -Xmx250m -classpath .;./sam-1.103.jar;./jbzip2-0.9.jar uk.ac.babraham.FastQC.FastQCApplication
Try opening the MS-DOS prompt, changing directory into the one the run_fastqc file is in and execute that command - does that work?
If that doesn't work, I would open up your run_fastq.bat file in Notepad - to check the exact command on your computer (you may have a different version to me) - and try that.
If not, you could try disabling Kaspersky, then trying FastQC, then turning Kaspersky back on: http://faq.mydocsonline.com/695/java-applications-cannot-launch-due-to-kaspersky-internet-security/
If not, prob time to try another tool
You need to be in the the fastqc directory (the directory run_fastqc bat file is in), and then run the command:
java -Xmx250m -classpath .;./sam-1.103.jar;./jbzip2-0.9.jar uk.ac.babraham.FastQC.FastQCApplication
So either cd into it, or launch the dos prompt from that folder directly:
http://www.techsupportalert.com/content/how-open-windows-command-prompt-any-folder.htm
NGS QC toolkit is good choose to quality control http://www.nipgr.res.in/ngsqctoolkit.html
RseqQC http://rseqc.sourceforge.net
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