Originally posted by flxlex
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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.
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Originally posted by GenoMax View Post@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.
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@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.
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Originally posted by [email protected] View PostHi,can anyone tell me how i can convert any fastq to BAM ?
Thanks
rinku
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Hi,can anyone tell me how i can convert any fastq to BAM ?
Thanks
rinku
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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.
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Why don't you just list the version you used and the command line?
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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.
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I find their manual and a table on page 28. I was wondering if this is the default settings.
Here is manual link
Please help me and see if the table on Page 28 is the assemble default settings.
thanks.
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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
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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,
BenTags: None
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