[simonandrews]

The download site still shows FastQC v0.1 even after clearing my cache. Am I missing something here?

Sorry, the download page copied over to the wrong folder. Try it again now and the links should be updated.

[simonandrews]

Hi! Thanks for sharing this program - I like the idea of getting a summary look at the FASTQ's

I tried from 3 different linux boxes, but get the same error :


java -Xmx250m -classpath . uk.ac.bbsrc.babraham.FastQC.FastQCApplication

Exception in thread "main" java.lang.NoClassDefFoundError: uk/ac/bbsrc/babraham/FastQC/FastQCApplication

If you're running the program from outside the install directory you need to set the classpath to the directory which contains the FastQC installation, eg:

java -Xmx250m -classpath /usr/local/FastQC uk.ac.bbsrc.babraham.FastQC.FastQCApplication

If you have a non-standard classpath on your machine (which you probably won't by default) you may need to append your existing classpath:

java -Xmx250m -classpath /usr/local/FastQC:$CLASSPATH uk.ac.bbsrc.babraham.FastQC.FastQCApplication

Hopefully that should get you up and running.

[NGSfan]

If you're running the program from outside the install directory you need to set the classpath to the directory which contains the FastQC installation, eg:

java -Xmx250m -classpath /usr/local/FastQC uk.ac.bbsrc.babraham.FastQC.FastQCApplication

If you have a non-standard classpath on your machine (which you probably won't by default) you may need to append your existing classpath:

java -Xmx250m -classpath /usr/local/FastQC:$CLASSPATH uk.ac.bbsrc.babraham.FastQC.FastQCApplication

Hopefully that should get you up and running.

Thank you Simon, the second command worked. I guess the classpath we have is non-standard!

FastQC works great! Very helpful tool - a great way to get a quick look at the data.

[simonandrews]

I've just put FastQC v0.2 up on our website. The main changes are:

1. Some basic colorspace support
2. An option to create unzipped reports directly as well as the original zip files
3. An option to customise the HTML reports to add your own site branding
4. Adding an easily parsed summary file to allow pipelines to quickly flag potential problems

There are also numerous smaller fixes to make things work more smoothly.

You can get the new version from:

http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/

[If you don't see the new version of any page hit control+refresh to force our cache to update]

[NGSfan]

I've just put FastQC v0.2 up on our website. The main changes are:

1. Some basic colorspace support
2. An option to create unzipped reports directly as well as the original zip files
3. An option to customise the HTML reports to add your own site branding
4. Adding an easily parsed summary file to allow pipelines to quickly flag potential problems

There are also numerous smaller fixes to make things work more smoothly.

You can get the new version from:

http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/

[If you don't see the new version of any page hit control+refresh to force our cache to update]

thanks for the update simon! those extra features are really good.

Some feature requests: could you add ability to

1) read in gzipped FASTQ files
2) be able to reload reports to view again

Thanks for this package - nice and convenient

[simonandrews]

1) read in gzipped FASTQ files
2) be able to reload reports to view again

I think 1 should be fairly easy to manage - I'll look into that for the next version.

I can't see why you'd want to do 2 though. If you save a report you get an HTML version which you can open immediately and which shows exactly the same information as you had in the interactive report, or am I missing something?

Simon.

[NGSfan]

I think 1 should be fairly easy to manage - I'll look into that for the next version.

I can't see why you'd want to do 2 though. If you save a report you get an HTML version which you can open immediately and which shows exactly the same information as you had in the interactive report, or am I missing something?

Simon.

You know what, you're right! scratch that then - I actually never got around to opening the gzipped reports, I just assumed they were image dumps, but HTML is even better.

Thanks Simon!

[RockChalkJayhawk]

I can't see why you'd want to do 2 though. If you save a report you get an HTML version which you can open immediately and which shows exactly the same information as you had in the interactive report, or am I missing something?

Simon.

There is only 1 small difference between the HTML and the actual analysis. The HTML form doesn't say what type of quality values were used but they show up when you run the program.

[martian_bob]

This is an excellent tool, wish I'd had it months ago!
Any chance you could add functionality for colorspace-based fastq files, produced by the solid2fastq script in BWA? Right now the per base sequence content, per base GC content, per sequence GC content, and per base N content tests aren't working for my reads.

[simonandrews]

There is only 1 small difference between the HTML and the actual analysis. The HTML form doesn't say what type of quality values were used but they show up when you run the program.

Sorry - that's a bug which I've just fixed in the development version. It will work the same in the HTML and interactive versions in the next release.

[simonandrews]

This is an excellent tool, wish I'd had it months ago!
Any chance you could add functionality for colorspace-based fastq files, produced by the solid2fastq script in BWA? Right now the per base sequence content, per base GC content, per sequence GC content, and per base N content tests aren't working for my reads.

Does the summary say that the file was recognised as colorspace or is it misreading it as conventional base calls?

Any chance you could let me have an example file which isn't working? We don't use SOLIDs here so I only have a small set of examples. Contact me off list ([email protected]) if you can help - I should only need a small fragment of the file to be able to figure out why it's not working.

[simonandrews]

FastQC v0.3 released

I've just put FastQC v0.3 up on our website. This should fix the problems with unrecognised colorspace files and adds back the type of quality score identified into the HTML report files.

There are a couple of new features. The main one is a system for identifying the source of any overrepresented sequences. The program now has a list of all of the primers and adapters commonly in use on sequencing platforms and will scan any overrepresented sequences to see if they match against these. If anyone has any other common sources of contamination they know of they can either add them to their local installation, or preferably pass them back to me so I can add them in to future versions of FastQC.

Another change is a new parameter which can be passed to the non-interactive version of the program to specify a non-default output directory for reports. This should help people who only have read-only access to the original sequence files, but still want to generate reports automatically.

Finally the program now supports the processing of gzip compressed fastq files, since some sites apparently compress their data for long term storage.

You can get the new version from:

http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/

[If you don't see the new version of any page hit control+refresh to force our cache to update]

[mard]

I've been using FastQC in interactive mode and it's a really great tool.

I just tried to install and run FastQC v0.3 in non-interactive mode but got this error below (I'm running it on a Mac 10.6).

$ java -Xmx250m -classpath /Tools/FastQC/ uk.ac.bbsrc.babraham.FastQC.FastQCApplication sequence.fastq
Processing sequence.fastq
Approx 5% complete for sequence.fastq
Approx 10% complete for sequence.fastq
Approx 15% complete for sequence.fastq
Approx 20% complete for sequence.fastq
Approx 25% complete for sequence.fastq
Approx 30% complete for sequence.fastq
Approx 35% complete for sequence.fastq
Approx 40% complete for sequence.fastq
Approx 45% complete for sequence.fastq
Approx 50% complete for sequence.fastq
Approx 55% complete for sequence.fastq
Approx 60% complete for sequence.fastq
Approx 65% complete for sequence.fastq
Approx 70% complete for sequence.fastq
Approx 75% complete for sequence.fastq
Approx 80% complete for sequence.fastq
Approx 85% complete for sequence.fastq
Approx 90% complete for sequence.fastq
Approx 95% complete for sequence.fastq
Approx 100% complete for sequence.fastq
Failed to process sequence.fastq :/Tools/FastQC/Templates/.svn

[simonandrews]

I just tried to install and run FastQC v0.3 in non-interactive mode but got this error below (I'm running it on a Mac 10.6).

Failed to process sequence.fastq :/Tools/FastQC/Templates/.svn

It's a bug in the templating system. There's a check which should stop anything other than image files getting added to the template, but looking again I see that it's not being applied correctly.

I'll put out an update which fixes this, but the temporary work round is to go into the Templates directory and do:

rm -r .svn

..which should fix the problem in the current version.

Sorry about that.

Simon.

[Bruins]

Dear Simon,

Thank you for the great software! I find the report to be very clear and informative. The docs on how to interpret the report are clear and very helpful. I will probably incorporate FastQC in my pipeline.

I had FastQC test one of my raw reads files. The file is approx. 4.5 GB (FastQC says 21107088 sequences) and all reads are 76 bases. It took FastQC about 5 minutes to process the file (I like the progress report!). Fast enough for me!

One problem did arise:

Failed to process -Dfastqc.output_dir=./fastqc/ :fastqc doesn't exist

I am pretty sure the dir does exist... it has permission drwxrwxr-x. (and checked for typo's :P).

Thanks for the hard work,

Wil