I got paired-end read with dual codebare in line. I used to demultiplexe my reads with 2 consecutives cutadapt rounds. It seems that qiime cutadapt demux-paired command can do this job. However, when I run it, it demultiplexes only the forward codebare. I don’t really know where i am worng. Is anyone can help me to fix it ?
Here an example of my manifest file (Metadata.csv):
Are you basing that on the filenames, or, by the nts present in the reads? If it is by the filenames, no need to worry there, the plugin is lazy and lists the forward barcode in both the forward and reverse files.
thermokarst
(Matthew Ryan Dillon)
unassigned thermokarst
#4
Thank you thermokarst for you answer. When I said it demultiplexe only the forward barecode I mean the BC1 (as the sample 2 and 4 seem to be mixed with the sample 1 and 3 respectively in my example). At least could you confirm that this kind of command can do this job in a single step? I have tried to put 2 seperated metadata file with only 1 column for each barecode (BC1 and BC2) but it doesn’t change anything.
Hi @Kap25, would you be able to send your data along, so that I can run the q2-cutadapt command above and debug locally? Feel free to DM me download links, if you don’t want to share publicly. Thank you!
thermokarst
(Matthew Ryan Dillon)
unassigned thermokarst
#8
thermokarst
(Matthew Ryan Dillon)
assigned thermokarst
#9
Thanks for sharing your data, @Kap25! I had a look at this and ran things locally, cutadapt (and q2-cutadapt) appear to be working as expected here. Can you double check that your barcodes in your metadata file are correct? If you run the demux command with the --verbose flag you will see a very detailed demux report with information about what barcodes were found, and how often they were found. Take a peek at that and double-check your metadata file. Thanks!
thermokarst
(Matthew Ryan Dillon)
unassigned thermokarst
#11