454 Short Primer Filter
1
0
Entering edit mode
13.7 years ago
Bdv ▴ 320

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

filter sequence primer • 3.4k views
ADD COMMENT
2
Entering edit mode

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

ADD REPLY
3
Entering edit mode
13.7 years ago
Casbon ★ 3.3k

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 COMMENT
2
Entering edit mode

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 REPLY
2
Entering edit mode

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

ADD REPLY
2
Entering edit mode

+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 REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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 REPLY

Login before adding your answer.

Traffic: 1553 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6