==> newbler and paired end

[Zimbobo]

Hello,

I have newbler and a few sff files that I would like to assemble. Problem is the documentation is very sketchy and I don't know which sff file is paired end and what the insert size is.

How can I find out?

Or is newbler able to figure it out?

Still I would like to have the information and make sure I am using newbler correctly.

Any suggestion?

Thanks.

[maubp]

The SFF file format doesn't care or know if the reads are paired end or not. However, the Roche "Newbler" tools are aware of the linker sequences and should spot this automatically.

If you are using something like MIRA which can't work directly from SFF files, the tool sff_extract is recommend. Essentially this searches each read for the Roche 454 pair end linker sequence and if found splits the read into a pair.

[Zimbobo]

Thanks for the input.

At the moment I really just want to make sure of what I have.

How can I find out which of my sff files are paired end libraries and what the insert size is?

Thanks.

[maubp]

Do you have the Roche "Newbler" off instrument applications?

[Zimbobo]

It appears for sff_extract I need a file with linker sequences. Anybody knows what those are?

[Zimbobo]

You mean sffinfo etc. Yes I do.

Do you have the Roche "Newbler" off instrument applications?

[maubp]

It appears for sff_extract I need a file with linker sequences. Anybody knows what those are?

You're not the first to ask this, did you even try searching the forum? e.g.

http://seqanswers.com/forums/showthread.php?t=12940

May I also point you at this useful read:

http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002202

[RCJK]

Also I'd think the easiest thing to do would be to ask your service provider which file is which.

[flxlex]

If you start a newbler assembly and give it all your files, in the very first stage it will read the files and report if they contain paired-end reads. You can then kill the program.

[Zimbobo]

Unfortunately the service provider doesn't exist anymore, that's one of the problems, I would have certainly done that first.

Also I'd think the easiest thing to do would be to ask your service provider which file is which.

[Zimbobo]

Thanks. That's useful information. It appears there are no paired-end files even though there should be, in other words, it looks like we didn't get all the data from the service provider (which doesn't exists anymore).

If there is still an idea around how to get a simple yes/no answer from 454 sff files as to whether they are paired-end or not (and if yes, what the insert size is), I'd be very interested in that.

Thanks again.

If you start a newbler assembly and give it all your files, in the very first stage it will read the files and report if they contain paired-end reads. You can then kill the program.