The command went through successfully, my issue is that the follow up command:
qiime cutadapt demux-paired
is for data that has the barcodes in the data ( --i-seqs ARTIFACT MultiplexedPairedEndBarcodeInSequence --- is the only artifact I found) and my data is not of that type.
My question is if after the import using the qiime cutadapt demux-paired is ok as the import "fixes" the data or I need to use a different command?
If I need to use a different command, what is it?
Thank you very much for your assistance
Nadav
Hi @nadavlisha,
It is alittle hard for me to decode because I dont have the error messages.
from what I understand qiime cutadapt demux-paired command doesn't seem to be what you are looking for. qiime cutadapt demux-paired is used for removing barcodes from within your sequence and demultiplixing.
That does help!
Now I have a different question (it’s not from due to an error but about the arguments in another command)
After I used the qiime demux emp-paired command on my data I want to use the following command: qiime cutadapt trim-paired
however I don't know what should I put in the following arguments:
--p-front-f
--p-front-r
ext.
the command I used for single paired (qiime cutadapt trim-single) used the following string in the --p-front argument: GCTACGGGGGG
what should I put in the arguments?
appreciate the help
Nadav
If you do have adapters in sequnces you will need to know the adapters that are in your sequence. I would recommend reaching out to the sequencer or the person who handed you the data to figure out what adapter sequence to remove.