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Old 12-29-2011, 11:43 AM   #1
asheenlevrai
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Default how to get rid of adapter sequences

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-

Last edited by asheenlevrai; 12-29-2011 at 11:49 AM.
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Old 12-31-2011, 02:04 PM   #2
nicedad
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What kind of data you've got?
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Old 12-31-2011, 04:37 PM   #3
asheenlevrai
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mRNA 5' end reads
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Old 01-01-2012, 08:24 AM   #4
ETHANol
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http://sourceforge.net/apps/mediawik...itle=Main_Page

The OSX binaries are posted somewhere here on SEQanswers.
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Old 01-03-2012, 06:46 AM   #5
nicedad
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you can use this also
http://edwards.sdsu.edu/prinseq_beta/
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