FastQ Screen: Does your library contain what you think it does?

[idonaldson]

Thanks - i got it working for color-space by changing:

my $path_to_bowtie = 'bowtie -C';

[simonandrews]

This looks pretty nice. As I understand it the user supplies the libraries to screen against - I wonder how one would go about to set up a library of adaptors/vectors/contaminants. Are there any commonly used collections of such sequences?

Yes, the sequences to screen against are left up to the user since different sets of sequences will be applicable for different facilities. If you look in the example config file shipped with the application then you can see in the comments the set of libraries we're using and where we got them from.

Basically I'm trying to cover the species which we're commonly working with in our institute plus vectors, adapters and other common sources of contamination (eg E.coli) which could come from any molecular biology lab.

Any suggestions for other sources to screen against would be welcome.

[gaffa]

This looks pretty nice. As I understand it the user supplies the libraries to screen against - I wonder how one would go about to set up a library of adaptors/vectors/contaminants. Are there any commonly used collections of such sequences?

[simonandrews]

Looks like a great tool. I am using colour space data, so when i use my colour space indexes i get the following message:

Error: -C was not specified when running bowtie, but index is in colorspace.

The current version of the script doesn't include colorspace support - I'll put that into the next release.

A quick fix would be to edit the script and just add -C to the list of bowtie options to force colorspace mode on all analyses. Let me know if this doesn't work and I'll send out a proper fix.

[idonaldson]

Colour space usage

Looks like a great tool. I am using colour space data, so when i use my colour space indexes i get the following message:

Error: -C was not specified when running bowtie, but index is in colorspace. If
your reads are in colorspace, please use the -C option. If your reads are not
in colorspace, please use a normal index (one built without specifying -C to
bowtie-build).

How do i specify this?

Apologies if this is simple, but it is Friday afternoon.

Ian

[simonandrews]

Sorry, I could not find the code.

Try pressing shift+refresh on our download page. Our downstream cache sometimes likes to hold on to old versions of some of our pages.

[ttnguyen]

Sorry, I could not find the code.

[simonandrews]

I've just released the first version of a simple little program which allows you to screen a FastQ file against a panel of sequence databases so you can quickly see if your libraries contain the types of sequence you think they do, and if not then what sources of contamination might be in there.

I take no credit at all for the idea behind this which I saw in the CRI QC pipeline, and which looked so useful I wrote an implementation for our sequencing facility. We've been running our historical data through it and we've already found a few issues we didn't know we had up until now.

The code is pretty new, so please use with caution, and file bugs if you hit problems.

You can see example output and get the code from:

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