Nextera data analysis recomendations

[jvanleuven]

Hello,

Can anyone recomend software for processing Nextera 100bp PE data.

I could take it through a series of adapter trimming steps, but it seems like there should be a tool that looks for external and junction adapters, then orients read pairs correctly.

Thanks

[Torst]

The software on the MiSeq (or HiSeq) can be configured to trim the adaptors for you.

I'm not sure why the read pairs would be oriented incorrectly though.

I use the "clip:" command in our "Nesoni" software to remove adaptors.
http://www.vicbioinformatics.com/software.nesoni.shtml

[jvanleuven]

The attached image is from illumina's "Data Processing of Nextera Mate Pair Reads"

I'm not sure how to tell the difference between templates (a) and (e) without a reference.

I can process these data with almost any adapter trimming software, but specific software would make it easier. If I write something, I'll post it.

Thanks

[Torst]

Is this brand new Nextera MATE PAIR or PAIRED END protocol reads?

As for overlapping problems, it's a balance of probability guess work: http://thegenomefactory.blogspot.com...aired-end.html

[jvanleuven]

Yes. Mate pair.

I haven't decided yet whether to write some software to handle these or not.

I can do it by carefully using adapter trimming software and discarding a higher proportion of reads, but I was hoping that somebody had already written something to properly handle them.

Thanks Torst. Also, I have the genome factory bookmarked, it's a great resource.