[robs]

I am not sure if this will identify the exact same adapters as FastQC, but take a look at TagCleaner (http://seqanswers.com/wiki/TagCleaner).
It might help if you provide the adapter sequence since you seem to be sure they are the TruSeq adapters. Depending on the file size, I would also suggest you try the standalone version as the web version is not well suited for large files.

[NextGenSeq]

We never run 150 cycle runs, the last 50 cycles are a waste of money

[tonybolger]

We never run 150 cycle runs, the last 50 cycles are a waste of money

It depends on the application for sure, and how nicely the machine is running. What Qs are you seeing in the last 50 base calls?

[simonandrews]

*BUMP*

I'm using FastQC as well (great program - thanks!) and I have noticed that I have significant contaminations of TruSeq adapters. Is there a program that will trim these without me having to specify the adapter sequences themselves? I.e. a program that uses the same sort of information as FastQC to automatically identify and trim them?

Thanks - and sorry for the bump!

I think TagDust does something along these lines - identifying and removing artificially overrepresented sequences.

I'd be careful how I applied this sort of analysis though. Depending on your experiment many of the Kmers identified by FastQC and similar programs may have a biological rather than a technical origin.

[kga1978]

Thanks for the link to TagDust - I'll have a look at that. For now though, I found a combination of cutadapt to remove adapters (the adapter sequence I took from the file inside the FastQC program) and prinseq to remove low-quality sequences works very well. A little slow, but it does clean up nicely some of my more messy alignments.

[simonandrews]

Thanks for the link to TagDust - I'll have a look at that. For now though, I found a combination of cutadapt to remove adapters (the adapter sequence I took from the file inside the FastQC program) and prinseq to remove low-quality sequences works very well. A little slow, but it does clean up nicely some of my more messy alignments.

Cutadapt can do quality trimming as well as adapter removal. It may not have as many options as Prinseq, but if it's good enough it might speed up your workflow a bit.

[vinay052003]

Hi,
When I want to run cutadapt or similar adapter trimming program, should I specify both of the Illumina PE adapters for each fastq file? How does program differentiate between the 5' and 3' adapter ?

[simonandrews]

Generally you shouldn't see the 5' adapter since the sequencing primer is complementary to the end of this adapter. You'd simply select the 3' adapter for whichever read you were trimming.

Having said this, the approach used by trim galore is to use the common sequence which is present at the end of all of the illumina adapters, so this should allow the removal of any of the adapters.