how to get rid of adapter sequences

[asheenlevrai]

Hello,

I received a dataset of reads that are supposed to have the following format:

bases (1-3) = 3bp fingerprint (I know what this sequence should be)
bases 4-28 = 25bp read
bases 29-36 = 8bp adapter sequence (I know what this sequence should be)

The fingerprint is OK and the 1st 3 bases where thus trimmed.

However, in many cases, the adapter sequence is a few bases longer or shorter than 8bp. Thus, trimming 8bases from the end results in reads that lack a few bases or that contain a few bases from the adapter...

In some reads, I can't find the adapter sequence... it seems like I have 25+8 bases of genomic sequence, but I'm not sure about that...

Is there a way to qualitatively trim the reads from the end, removing all (but only) the adapter sequence?

Thanks a lot for your help
-a-

[nicedad]

What kind of data you've got?

[asheenlevrai]

mRNA 5' end reads

[ETHANol]

http://sourceforge.net/apps/mediawiki/theflexibleadap/index.php?title=Main_Page

The OSX binaries are posted somewhere here on SEQanswers.

[nicedad]

you can use this also

http://edwards.sdsu.edu/prinseq_beta/