454 Short Primer Filter

Question

[Bdv]

Hi I received many reads failed in 454 amplicon sequencing because of short primer, What does it mean? Thank you!

[Thaman]

please elaborate your question precisely, mention what you did, want you to achieve and problems you faced.

Answer 1

[Casbon]

RTFM (see edits for links):

3.2.2.1.5 The Primer Filter

The ends of all processed reads are scanned for similarity to Genome Sequencer System Adaptor sequences. Any flows corresponding to Adaptor sequences are trimmed from the read. If a trimmed read is shorter than 84 flows (21 cycles, or approximately 50 nucleotides), it is rejected. The output metric for these failed reads is “numTrimmedTooShortPrimer”.

PS is it harmful to answer a negatively rated question!

PPS I think there is enough to answer the question in the question

Edit manual links (v2.3):

• http://sequence.otago.ac.nz/download/ManualPartB.pdf
• http://sequence.otago.ac.nz/download/ManualPartC.pdf
• http://sequence.otago.ac.nz/download/ManualPartD.pdf
• http://sequence.otago.ac.nz/download/ManualPartE.pdf

I actually think 2.0 was better laid out, but I can't find a link. Contact your roche rep and ask for a u/p to the Roche FTP site.

[Michael]

reg. PS: no, to the contrary it will improve your carma reg. PPS: maybe, but it was poorly written anyway i believe

+1 for RTFM

[Casey Bergman]

-1 for RTFM, the use of insulting acronyms is anathema to a civil public forum.

[User 59]

+1 for RTFM, it saves a lot of time and effort, and is suitably venerable enough a part of internet vocabulary to not be insulting I think.

[Casey Bergman]

-1 for RTFM, the use of insulting acronyms is anethema to a civil public forum.

[Michael]

Casey, what the #$& is insulting in Read The Fine Manual*??? :D

[Michael]

Casey, what exactly is that insulting in Read the Fine Manual ??? lol

[Michael]

Casbon, can you post a link to the fine Manual? I think, one reason to explain these kin of questions is that not everyone who is asked to analyse that kind of data has access to the manuals. Sad but true, Roche.