quality read software

Question

[nora]

hello

I need a free software that work with no connection and containing the tool fastqc

Answer 1

[Antonio R. Franco]

FaatQC does not need an Internet connection to work. You only need it to get the program

[nora]

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

[Medhat]

what version of java you have?

[Antonio R. Franco]

There are two flavors of Java, 32 and 64 bits Check if you have installed the 64bit version

[nora]

i verified the java instalation (64 bit), but the problem is still

[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

[nora]

it directly closes the program after execution

[Antonio R. Franco]

If using Windows, notice that a cmd window is opened. Within this window, you get verbose information about what is happening

[nora]

the information of cmd C:\Users\HP>java -version java version "1.8.0_111" Java(TM) SE Runtime Environment (build 1.8.0_111-b14) Java HotSpot(TM) Client VM (build 25.111-b14, mixed mode, sharing)

[Tonor]

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

[nora]

yes i need fastqc only , To do a job for students ( this time I used the Galaxy interface)

[Tonor]

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.

[nora]

yes i installed the fastqc and the java ( for windows 10 , 64bits)

Kaspersky is able to block the execution of java, although I save as a sure object, but the problem is the same

[Tonor]

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?

[nora]

does not work ( close directly)

[Tonor]

So no error messages get sent to the DOS prompt? And no message from Kaspersky? When you type:

java -Xmx250m -classpath .;./sam-1.103.jar;./jbzip2-0.9.jar uk.ac.babraham.FastQC.FastQCApplication

[nora]

yes Erreur : impossible de trouver ou charger la classe principale uk.ac.babraham.FastQC.FastQCApplication

Unable to find or load main class

[Tonor]

Are you in the correct folder? You need to be located in the FastQC folder (wherever you downloaded it to on your computer).

This folder contains the file run_fastqc.bat file, sam-1.103.jar, and loads more

[Tonor]

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

[nora]

thank you very much for your help

[nora]

yes it contains this file, the fastqc are downloaded directly in my computer (I tried several times to install it)

[Tonor]

If you type:

dir

Into the dos prompt what is the output?

[nora]

is a list of many program ( without fasqtc)

[Tonor]

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

Answer 2

[reza]

NGS QC toolkit is good choose to quality control http://www.nipgr.res.in/ngsqctoolkit.html

Answer 3

[Ron]

RseqQC http://rseqc.sourceforge.net