Newbler default settings? -- Any papers

[SDPA_Pet]

Hi, I assembled my 454 metagenomic seqs with Newbler default setting. In my manuscripts, I wrote "assembled using Newbler with default settings. The reviewers asked me to list some details. I search a lot of papers. They all write same as me assembled with Newbler with default settings.

Can anyone find a paper for me with using 454 metagemonics sequencings and list some details with default setting. It doesn't have to be really detailed info.

Thanks,
Ben

[SDPA_Pet]

Newbler default settings? -- Any papers

Hi, I assembled my 454 metagenomic seqs with Newbler default setting. In my manuscripts, I wrote "assembled using Newbler with default settings. The reviewers asked me to list some details. I search a lot of papers. They all write same as me assembled with Newbler with default settings.

Can anyone find a paper for me with using 454 metagemonics sequencings and list some details with default setting. It doesn't have to be really detailed info.

Thanks,
Ben

[SDPA_Pet]

I find their manual and a table on page 28. I was wondering if this is the default settings.

Here is manual link

http://454.com/downloads/my454/documentation/gs-flx-plus/454SeqSys_SWManual-v2.6_PartC_May2011.pdf

Please help me and see if the table on Page 28 is the assemble default settings.

thanks.

[Bukowski]

If you run Newbler at the command line it will probably spit out a help screen, and the default values, most command line tools will do this.

[Brian Bushnell]

Why don't you just list the version you used and the command line?

[SDPA_Pet]

Well, I was using GUI version.

[maubp]

As long as you list the full version number, I agree "default parameters" ought to be enough.

(The reasoning being defaults and settings do change, so without the version number you can't infer the settings - moreover without the version number you would struggle to get the same results even if the settings hadn't changed).

If this was at the command line, you could give the actual command in your supplementary materials to appease the reviewers.

[[email protected]]

Hi,can anyone tell me how i can convert any fastq to BAM ?

Thanks
rinku

[maubp]

Hi,can anyone tell me how i can convert any fastq to BAM ?

Thanks
rinku

That has nothing to do with this thread about Newbler default settings. Please search the forum - this is probably a read mapping question.

[GenoMax]

@SDPA_Pet: Even though you used the GUI, newbler probably wrote a log file somewhere of what was happening. Find and look through that file to see if you can get the command line/options the program used.

[SDPA_Pet]

@SDPA_Pet: Even though you used the GUI, newbler probably wrote a log file somewhere of what was happening. Find and look through that file to see if you can get the command line/options the program used.

I am using Newbler 2.6. Can you check the link that I paste. Is the table on Page 28 listing the default settings?

[flxlex]

The page you mention contains the default settings, yes. Unfortunately, you can't get these from the log files.

However, I agree with @maubp that the reviewer's request is nonsensical. What is the point of describing parameters if you don't change them? Newbler has a few dozen parameters, if you really want to spend a lot of time, see section 4.1 in the same PDF.

[SDPA_Pet]

The page you mention contains the default settings, yes. Unfortunately, you can't get these from the log files.

However, I agree with @maubp that the reviewer's request is nonsensical. What is the point of describing parameters if you don't change them? Newbler has a few dozen parameters, if you really want to spend a lot of time, see section 4.1 in the same PDF.

Thanks. I know it's nonsense. So, if I don't want to give them these default settings, how should I reply them? You know, you are supposed to answer all the reviewers concerns.