Find adapter sequence

[guilhem]

Hi,
I would like to remove the adapters from a RNA-seq reads of many studies. I download the reads from GEO NCBI. In some case, the sequence adapter is specified (sometime I have to go through the paper) and in other they are not specified at al.
e.g. http://www.ncbi.nlm.nih.gov/geo/quer...acc=GSM1918965

Here for instance, I tried to this adaper CTGTAGGCACCATCAAT with this fastx_clipper

fastx_clipper -Q33 -a CTGTAGGCACCATCAAT -l 25 -c -v -z -n

However, it seems that it is not the good adapter since only 15,000 reads are remaning.

Is there a way to find the sequence adapter when not specify in the study and without spending time to go through the paper?

(I am ok to use any other software like cutadapt etc..)

Thanks

[Brian Bushnell]

BBDuk comes with a file containing all common Illumina adapters in /bbmap/resources/adapters.fa. You can trim the reads using all adapters at once, as indicated in the first post.

[guilhem]

Thank a lot Brian! It works perfectly well and it is SO fast, I can't believe it, I will definitely use it instead of fastx!