Newbler vector trimming issue

andylai · 11-30-2010, 10:50 PM

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

flxlex · 12-01-2010, 12:20 AM

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!

andylai · 12-01-2010, 03:51 AM

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 · 12-01-2010, 03:52 AM

If I did not use -vt in the second time, runAssembly can not import the primerdatabase for removing primers.

flxlex · 12-03-2010, 07:14 AM

Quote:

Originally Posted by andylai

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.

zhengz · 08-30-2011, 06:54 AM

Hi andylai,

Have you solved this problem? The problem seems to persist in v2.6.

kopardev · 01-06-2012, 01:33 PM

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.

vamosia · 01-10-2012, 11:16 AM

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.

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11-30-2010, 10:50 PM	#1
andylai Junior Member Location: Australia Join Date: Apr 2010 Posts: 6	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

12-01-2010, 12:20 AM	#2
flxlex Moderator Location: Oslo, Norway Join Date: Nov 2008 Posts: 415	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!

12-01-2010, 03:51 AM	#3
andylai Junior Member Location: Australia Join Date: Apr 2010 Posts: 6	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.

12-01-2010, 03:52 AM	#4
andylai Junior Member Location: Australia Join Date: Apr 2010 Posts: 6	If I did not use -vt in the second time, runAssembly can not import the primerdatabase for removing primers.

08-30-2011, 06:54 AM	#6
zhengz Member Location: sweden Join Date: Aug 2010 Posts: 23	Hi andylai, Have you solved this problem? The problem seems to persist in v2.6.

01-06-2012, 01:33 PM	#7
kopardev Member Location: VA, USA Join Date: Oct 2011 Posts: 18	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.

01-10-2012, 11:16 AM	#8
vamosia Member Location: New York Join Date: Mar 2009 Posts: 15	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.