I was wondering if anyone knows or has an idea about whether you could analyze dual-index sequences without joining paired ends? If you use dual-index sequencing, but later decide to only use the forward reads, for example, would this be ok? Thanks in advance for the input!
Sure you can. Just because you scrap the reverse reads (e.g., because they are too short after trimming) does not mean you should scrap the dual-index benefits! (unless if the index reads are bad too).
QIIME 2 offers dual-index support in the q2-cutadapt plugin; see the docs for more details.
Ok great, thank you for the feedback!
@rlhughes correction: DI support is already available via q2-cutadapt! (maybe you are already aware, I had forgotten that this already was released!) I have edited my post above for clarity.
@Nicholas_Bokulich thank you! Sorry, but I’m not quite clear on how cutadapt demux-paired would differ for dual-index sequences based on the documentation provided above. How would you adapt the workflow compared to single-index sequences? Thank you for your help.
There is a required
forward-barcodes-column that must always be used.
There is an optional
reverse-barcodes-column that can be used in the event that you have DI sequences.
Note this only works if the barcodes are in the sequences, not if they are contained in a separate file (maybe that is the source of your confusion?)
Got it yes, thank you!