Remove adapter sequence

[vini]

Hi,

I am a newbie in the field of RNA-Seq and i apologize if this query seems too trivial. I have Solid data in fasta format and i am supposed to remove the P2 adapter.

The P2 adapter sequence is:
5' ------- (-) AGAGAATGAGGAACCCGGGG CAGTT--- - 3'
3' ------- (-) TCTCTTACTCCTTGGGCCCC GTC----- - 5'

Does this mean that the
5' ------(-) AGAGAATGAGGAACCCGGGG CAGTT--- -3' will be present at the 3'end of the reads while the
3' ------- (-) TCTCTTACTCCTTGGGCCCC GTC----- - 5' would be present at the 5'end of the read?

Thanks,
vini

[KevinLam]

When you say fasta format did you mean you converted the solid raw data from csfasta to fasta?

That's generally not advised as it may introduce errors into your reads if there's an upstream miscall on the cs base.