Mixed_oriented_reads

colinbrislawn · September 29, 2018, 5:48pm

Unfortunately, Qiime 2 does not have a built-in method for dealing with these.

reorient/demux mixed-orientation reads

opened 04:03PM - 04 Jan 18 UTC

closed 11:19PM - 17 Jun 20 UTC

**Current Behavior** - reads are in mixed orientation (both R1 and R2 reads con…tain forward/reverse reads) - reads also often contain barcodes - reads also probably contain primers Sounds like this is the output produced by at least one company, so may want to provide support for this. **Proposed Behavior** 1. add method to demux "mixed orientation" read format in one step 2. add a method to reorient reads (I think this may make more sense to allow a modular pipeline of import as paired-end --> reorient reads --> extract barcodes --> trim primers) **References** [raised on forum](https://forum.qiime2.org/t/problem-with-demux/2402?u=nicholas_bokulich)

You can deal with these outside of QIime then import, but I might be outside the scope of your question. There is some more advice over here:

May I ask how you came in position of mixed-origination reads? Most Illumina reads are one way.

Colin