clip 454's adapter?

[louis7781x]

Hi everyone,recently I analyzed roche 454 data ,I had a question,what is adapter of 454's data?

Because i want to clip adapter,I found FASTX-Toolkit that can do it;the FASTA/Q Clipper default is dummy adapter.

Can i use default?

My other question is that llumina's data also use dummy adapter?


If anyone Know the answer;Please tell me. Thanks!!!!!

Best regard

[kmcarr]

Typically you should not have to do this. The normal output of the Roche/454 data processing software has already trimmed the keytag from the 5' end and the B adapter (if any) from the 3' end of the reads. Only if your sequence provider has given you untrimmed reads (again this is very unlikely) would you need to worry about trimming 454 specific sequences.

[louis7781x]

Thanks!! But I also want to ask,It have already clip adapter of illumina's data too??

[kmcarr]

Thanks!! But I also want to ask,It have already clip adapter of illumina's data too??

The Illumina data processing pipeline does not do any read trimming, either adapters or low quality. That said, it should be very rare to find Illumina adapter sequence in your reads. You will only find Illumina adapter sequence in your reads in two circumstances; primer-dimers or library fragments which were too short (i.e. shorter than your read length). Even though these events should not occur, the do to a lesser or greater extent. (If they are happening to a greater extent have a long talk with your sequencing service provider.)

You can use tools such as fastx_clipper (part of the FastX Toolkit) or cutadapt to deal with these situations.

[louis7781x]

Thanks!!!!