[ronton]

The apt-get is nice since it installs into PATH. Thank you again.

[simonandrews]

The apt-get is nice since it installs into PATH. Thank you again.

If you want that from the manual install then you can just create a symlink in /usr/local/bin/ to wherever you installed fastqc, ie:

cd /usr/local/bin/
sudo ln -s /wherever/you/put/fastqc/fastqc .

[ronton]

I used sudo apt-get remove fastqc to uninstall the older version, and then used the commands above to create a link within /usr/local/bin to the /FastQC directory. This works.

However, when I attempt to execute the command 'fastqc' elsewhere, I receive this error:

The program 'fastqc' is currently not installed. You can install it by typing:
sudo apt-get install fastqc

If I go to the directory /FastQC or the symlinked directory /usr/local/bin/FastQC and type './fastqc' I receive the following message:

bash: ./fastqc: Permission denied

If I type 'perl fastqc' the interactive version loads perfectly, but I can only type this command from the /FastQC folder.

Something about permissions perhaps, I am not exactly sure, but I appreciate your help. I can still use the newest version which is what's important.

[GenoMax]

You may need to add execute permissions to the fastqc link and/or original executable. You can start by

$ sudo chmod u+x /usr/local/bin/fastqc

If that alone does not work then add the execute permission to the original location where the fastqc program is by substituting that path in the above command.

FastQC is a Java program. "perl fastqc" is probably ignoring first part of the command and running fastqc. Note to self. Think before posting, late on a friday.

[ronton]

Those did not seem to work, I don't know. The script fastqc is a perl script that runs the java command.

I did put in a bug tracker request to update apt-get.

[GenoMax]

Perhaps you need to adjust the location of your system perl in the FastQC script. Can you check if the current setting agrees with what you have ($ which perl)?

[Fernas]

Hi All,

How to cite FASTQC in my journal paper? is it published somewhere? or we just refer to the URL of the tool?

Regards,

[simonandrews]

I used sudo apt-get remove fastqc to uninstall the older version, and then used the commands above to create a link within /usr/local/bin to the /FastQC directory. This works.

However, when I attempt to execute the command 'fastqc' elsewhere, I receive this error:

The program 'fastqc' is currently not installed. You can install it by typing:
sudo apt-get install fastqc

OK, there's one, and possibly two things to sort out.

Firstly the permissions on the fastqc launch script aren't right and will need to be set so that it's executable. This might be everything you need to do.

To fix this move to the directory where you unzipped the FastQC installation and run the following command:

chmod 755 fastqc

..then try running fastqc again and see if it works.

The other issue you might have is that there is a stub for fastqc installed by your OS which is being found before the symlink you created. If fastqc isn't working after the first fix can you run:

which fastqc

..hopefully this should point to /usr/local/bin/fastqc, but if it doesn't can you post the location it gives, along with the results of:

echo $PATH

[simonandrews]

How to cite FASTQC in my journal paper? is it published somewhere? or we just refer to the URL of the tool?

Just cite the project URL. We keep having good intentions to put out a paper, but it keeps not happening...

[TimK]

Hi all,

I recently tried the new FastQC version and it's a great tool. My problem is I used it on RNA-Seq expression data and the resulting graphs look different from what I expected reading the manual and tutorials.

This is one of my experiment samples after adapter trimming and processing. Especially the per base sequence content and per sequence GC content look wrong for me. Does anyone have an idea what might be the reason for those graphs? The sequence duplication graph is also weird but I guess that's due to expression bias of genes. Could the other graphs also be caused by those?

Thanks and keep up the nice work
Tim

[simonandrews]

Hi all,

I recently tried the new FastQC version and it's a great tool. My problem is I used it on RNA-Seq expression data and the resulting graphs look different from what I expected reading the manual and tutorials.

This is one of my experiment samples after adapter trimming and processing. Especially the per base sequence content and per sequence GC content look wrong for me. Does anyone have an idea what might be the reason for those graphs? The sequence duplication graph is also weird but I guess that's due to expression bias of genes. Could the other graphs also be caused by those?

Thanks and keep up the nice work
Tim

Hi Tim - Yes, there's definitely something odd going on in that sample. It looks like there are a couple of specific sources of contamination. Having blasted the top hits in your overrepresented sequences list you get a hit to Methylmicrobium sp which might indicate that there's bacterial contamination (unless this is where the library comes from to start with?), otherwise you could be having problems with rRNA or other high abundance RNAs. The duplication graphs always look bad for RNA-Seq so that's not an issue, but the GC and base composition plots shouldn't look like that.

Simon.

[simonandrews]

Actually - the duplication also looks wrong. You expect a lot of high level duplication, but the scoop upwards in the 10k+ category isn't normally there, so that would fit with a high content contaminant.

[TimK]

Hi Simon,

thank you very much for the fast answer. The sample actually is a bacterial sample form a close relative of the blast result. I also guessed contamination but all reads I checked so far seem to come almost exclusively from the library organism. Then I thought about rRNA but not only should that have been removed before sequencing but I also used to remove remaining rRNA with sortMeRNA. That's why I'm a little lost atm.

But thanks for the effort. Will have to search for other contaminants then.
Cheers,
Tim

[ronton]

OK, there's one, and possibly two things to sort out.

Firstly the permissions on the fastqc launch script aren't right and will need to be set so that it's executable. This might be everything you need to do.

To fix this move to the directory where you unzipped the FastQC installation and run the following command:

chmod 755 fastqc

..then try running fastqc again and see if it works.

The other issue you might have is that there is a stub for fastqc installed by your OS which is being found before the symlink you created. If fastqc isn't working after the first fix can you run:

which fastqc

..hopefully this should point to /usr/local/bin/fastqc, but if it doesn't can you post the location it gives, along with the results of:

echo $PATH

I tried chmod 755 fastqc (and using sudo before it) and I get the same result.

'which fastqc' does not return anything, with or without sudo before.

echo $PATH returns

/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games

In the meanwhile I can use the interactive version of FastQC rather than command line, or I can also use apt-get install fastqc to use the command line with a previous version until the bug tracker updates to the latest version.

[simonandrews]

I tried chmod 755 fastqc (and using sudo before it) and I get the same result.

'which fastqc' does not return anything, with or without sudo before.

echo $PATH returns

/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games

In the meanwhile I can use the interactive version of FastQC rather than command line, or I can also use apt-get install fastqc to use the command line with a previous version until the bug tracker updates to the latest version.

Sorry for the slow repsonse - just got back from holiday.

It looks like the apt-get suggestions are happening at a higher level than the shell, so the fix will simply be to install the version of fastqc you installed into your path. Assuming you installed fastqc in /FastQC (as you said above) then the commands you'd need would be:

cd /usr/local/bin
sudo ln -s /FastQC/fastqc .

You'll be asked to enter your password after the second command. Also note that the second command needs the trailing dot at the end of the command. This should then allow you to run fastqc from everywhere. After you've run it you will need to close and re-open your shell before it takes effect.