Question: 454 Short Primer Filter
0
gravatar for Bdv
8.8 years ago by
Bdv310
Bdv310 wrote:

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

filter sequence primer • 2.0k views
ADD COMMENTlink modified 6.1 years ago by Biostar ♦♦ 20 • written 8.8 years ago by Bdv310
2

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

ADD REPLYlink written 8.8 years ago by Thaman3.2k
3
gravatar for Casbon
8.8 years ago by
Casbon3.2k
Casbon3.2k wrote:

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):

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.

ADD COMMENTlink modified 8.8 years ago • written 8.8 years ago by Casbon3.2k
2

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

ADD REPLYlink written 8.8 years ago by Michael Dondrup47k
2

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

ADD REPLYlink written 8.8 years ago by Casey Bergman18k
2

+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.

ADD REPLYlink written 8.8 years ago by Daniel Swan13k

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

ADD REPLYlink written 8.8 years ago by Casey Bergman18k

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

ADD REPLYlink written 8.8 years ago by Michael Dondrup47k

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

ADD REPLYlink written 8.8 years ago by Michael Dondrup47k

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.

ADD REPLYlink written 8.8 years ago by Michael Dondrup47k
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