SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > 454 Pyrosequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
newbler quality trimming Himalaya 454 Pyrosequencing 2 08-22-2012 04:44 AM
Please Help: What is the differences between standard trimming and adaptive trimming byou678 Bioinformatics 8 08-22-2011 12:05 PM
Vector contamination? gconcepcion Illumina/Solexa 5 02-08-2011 05:14 AM
Vector trimming: are flanking sequences sufficient? sulicon Bioinformatics 1 09-20-2010 07:02 AM
trimming issue malatorr 454 Pyrosequencing 3 01-25-2010 11:16 PM

Reply
 
Thread Tools
Old 11-30-2010, 09:50 PM   #1
andylai
Junior Member
 
Location: Australia

Join Date: Apr 2010
Posts: 6
Default Newbler vector trimming issue

Hi all,

I put a suspected 3' primer into trimming database fasta file, looks like this
>trim_vector1
ACGAGCGGCCA

But when I running runAssembly with correct -vt path, it still indicate warning message:
Warning: Suspected 3' primer ACGAGCGGCCA, 52012 exact matches found.

Newbler would not display warning about others primers that I added in trimming database,
I am very confusing why Newbler only keep going give warning about this primer.

Could anyone give an explain? Whether it's a bug. I am using Newbler v2.3
andylai is offline   Reply With Quote
Old 11-30-2010, 11:20 PM   #2
flxlex
Moderator
 
Location: Oslo, Norway

Join Date: Nov 2008
Posts: 415
Default

Strange. the adapters are still present in the contis?

Two things come to mind:
- you can only use the -vt option once, trying multiple -vt's will result in newbler using only one of them (can't remember if it was the first or last file when I did this)
- check the 454NewblerProgress file to see if newbler reports on having found your input file


Hope this helps!
flxlex is offline   Reply With Quote
Old 12-01-2010, 02:51 AM   #3
andylai
Junior Member
 
Location: Australia

Join Date: Apr 2010
Posts: 6
Default

Thanks for reply. I am not quite sure what do you mean -vt can only use one time. Now I got the out put result.
I tried to use:
cat 454AllContigs.fna | grep 'ACGAGCGGCCA'|wc -l

It get back result around 70. I think that means the adapter sequences still there in the result.
andylai is offline   Reply With Quote
Old 12-01-2010, 02:52 AM   #4
andylai
Junior Member
 
Location: Australia

Join Date: Apr 2010
Posts: 6
Default

If I did not use -vt in the second time, runAssembly can not import the primerdatabase for removing primers.
andylai is offline   Reply With Quote
Old 12-03-2010, 06:14 AM   #5
flxlex
Moderator
 
Location: Oslo, Norway

Join Date: Nov 2008
Posts: 415
Default

Quote:
Originally Posted by andylai View Post
Thanks for reply. I am not quite sure what do you mean -vt can only use one time.
I mean something like this:

runAssembly -o name -vt primers1.fasta -vt primers2.fasta *.sff

In this case, either the first or second file will be used, but not both.
flxlex is offline   Reply With Quote
Old 08-30-2011, 05:54 AM   #6
zhengz
Member
 
Location: sweden

Join Date: Aug 2010
Posts: 23
Default

Hi andylai,

Have you solved this problem? The problem seems to persist in v2.6.
zhengz is offline   Reply With Quote
Old 01-06-2012, 12:33 PM   #7
kopardev
Member
 
Location: VA, USA

Join Date: Oct 2011
Posts: 18
Smile

I encountered the same problem recently. The only way around was to trim the 3' adapter from the sff file using biopython and use the new trimmed sff file for assembly. This worked perfectly.
kopardev is offline   Reply With Quote
Old 01-10-2012, 10:16 AM   #8
vamosia
Member
 
Location: New York

Join Date: Mar 2009
Posts: 15
Default

You'll need to combined all the primer into one file. i.e

cat primers1.fasta primers2.fasta > primers.fasta

then used the combined primer file

runAssembly -o name -vt primers.fasta *.sff

my suspicious is newbler is only accepting on of -vt options but not both.
vamosia is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 01:30 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO