small RNA Seq adapter trimming

[paolo.kunder]

Dear All,
I am new to small RNA Seq data.
I have just received data and before I map my samples I would like to remove 5 and 3' adapters.
Here is my FastQC output, is similar in all samples:

sequence	count	percentage	possible source
GGCTGGTCCGATGGTAGTGGGTTATCAGAACTAGATCGGAAGAGCACACG	4842248	56.89688396826158	No Hit
GGCTGGTCCGATGGTAGTGGGTTATCAGAACCAGATCGGAAGAGCACACG	496150	5.829810654236004	No Hit
GGCTGGTCCGATGGTAGTGGGTTATCAGAACTTAGATCGGAAGAGCACAC	250074	2.9383937711325494	No Hit
GGCTGGTCCGATGGTAGTGGGTTATCAGAACAAGATCGGAAGAGCACACG	226967	2.6668842784641402	No Hit
GGCTGGTCCGATGGTAGTGGGTTATCAGAACAGATCGGAAGAGCACACGT	204732	2.4056208704283897	No Hit
TGAGGTAGTAGTTTGTGCTGTTAGATCGGAAGAGCACACGTCTGAACTCC	82348	0.9675969923511569	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTAGATCGGAAGAGCACACGTCTGAACTCC	65591	0.7707006159870881	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TAGCTTATCAGACTGATGTTGACAGATCGGAAGAGCACACGTCTGAACTC	56948	0.6691445271337941	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTAGATCGGAAGAGCACACGTCTGAACTCC	45012	0.5288953686757453	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)

There's something wrong?
Data is 50 bp x single read.
What are all these over-represented sequences? The first more than half of all reads!
Any suggestion?

Many Thanks

paolo

[GenoMax]

Have you blasted them to see what shows up? Your RNA would be expected to be small so scan/trim as you normally would.

[paolo.kunder]

Exactly. It match a pretty conserved intronic region of 32 bp in multiple species..
I assume this is spike in..

[GenoMax]

Can you scan/trim first and then check what remains?

[paolo.kunder]

I did it, i trimmed adaptor from my reads and blasted.
90% of my reads blast an intronic region conserved in multiple species..

[GenoMax]

Is this data from a monkey? That top sequence looks to be from one.

[paolo.kunder]

No human unfortunately......

[GenoMax]

Could this be some kind of contamination (if it is in all samples)? Perhaps talk with the owner of the data to see if there is any other logical explanation.

[paolo.kunder]

Dont you think that this is the spike in from Exiqon that was added in the samples?

[GenoMax]

I am not familiar with Exiqon but if it was indeed a spike-in would it to be > 50% of total reads?

[paolo.kunder]

Ops I was wrong, my data is full of yRNA, no idea why...and what they are..

[GenoMax]

Y RNA as in this entry?