When Uchime is called by chimera.uchime in reference-based mode, is it called with “-strand both”?
We follow the defaults - from the open source help output…
Reference database in FASTA format.
Optional, if not specified uchime uses de novo mode.
WARNING The database is searched ONLY on the plus strand.
You MUST include reverse-complemented sequences in the database
if you want both strands to be searched.
Although when I run the open source version with --strand both I think it works (not sure if it actually does it). We don’t seem to have an option flag for this in mothur, but we’ll go ahead and add it for the next release.
you could also upload the 16S Gold database reference, which contains Forward and Reverse sequences.
see USearch Download
It’s in the latest release from this past week
In 454 SOP, chimera.uchime section, reference=silva.gold.align is used.
Does this mean my sequences will be checked using one strand? How to change it? Hopeful parameter “strand” is listed, but without any description how to use it.
The file silva.gold.align is dated 23.07.2010, what is actually it’s source?
Is “16S Gold database reference” gold.fa file this:
gold.fa contains both strands, is silva.gold.align identical, except the second strand?
Ours is aligned and only has one strand. I should add, that you should really know what strand your sequences are in and put them in the correct direction using the flip=T and reverse.seqs options/commands in the SOP.
Thanks a lot.
I was not using SOP step by step, since I only have the access to fasta file. I wanted to check quickly for chimeras, but you are right I should go back few steps, and order the sequnces better.
Still, it would be great to know what is parameter “strand” in chimera.uchime?
Also, you mentioned that the file was added to then-the latest release (Jan 2013)? I can’t seem to find a reference file which was added this year. Probably I’m missing something?
The file has been in there for a long time. The strand option is new.
What do you mean by:
I have a dataset with a few ‘groups’, some are in a sense but the others in the other sense…
I have some troubles to easily reverse only the good sequences. Is there an easy way to do it with mothur commands ?
Well if you’re to the point of the SOP where you are using chimera.uchime, all of your sequences should be in the correct direction (align.seqs with flip=T will put them in the correct direction if they aren’t already). When you do 454 or Illumina sequencing, you know which direction you are sequencing because you define the sequencing primer and you know which end it is at. So… you should really know what strand your sequences are in.
Thank you for the answer!
I have this information but I am looking for a easier/quicker way to get all the sequences in the same sense.