How to remove illumina PCR primer 2.01 from RNA-seq samples

Question

[Fluorine]

I have RNA-seq samples that are highly contaminated with Illumina PCR primer 2.01, which program is best to use to remove those?

Answer 1

[michael.ante]

I'd recommend bbduck from the BBMap suite. It has included a lot of adapters and primer sequences, is very fast, and you can trim next to adapters also low-quality tails. Additionally, it is keeping your paired-end data in the correct order (if one read is removed, the other is removed too).

[GenoMax]

bbduk.sh (I make that mistake too). Adapters are in "adapters.fa" file in "resources" directory.

Answer 2

[Benn]

Trim Galore worked for me.

http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/

Answer 3

[Juke34]

cutadapt is also a nice one.

http://opensource.scilifelab.se/projects/cutadapt/

[ramonaramonawan]

To Juke-34. I have tried, but seems I could get the 3´primers cut off, I use the command cutadapt -a <reverse primer="" sequence=""> o <output name=""> directory/input file for the reverse primer sequence I hoped to cut, I tried the either the exact sequence of from 5´to 3´, or the reverse complementary one (the same as reverse primer as we order), both did not work. So any suggestions?

Thanks Ramona

[Juke34]

For reverse primer I guess the parameter is something like -A instead of -a. Did you read carefully the User Guide documentation ?
Everything is well explained with examples.

[adi.rotem]

for the 5' you need to use -g instead of -a. also sometimes the 5' adapters have more mistakes, so you can change the error rate (-e 0.2 allows 20% mistakes. 10% is the default)