Hi everyone,
I am new to using qiime. I have installed qiime2 and using it through my biomix account. I have got raw fastq.gz file for microbial analysis. I do not have barcodes file. I am following the moving picture tutorial to start doing analysis. My code is :
qiime tools import \
--type EMPSingleEndSequences \
--input-path emp-single-end-sequences \
--output-path emp-single-end-sequences.qza
it shows error as : There was a problem importing emp-single-end-sequences:
Missing one or more files for EMPSingleEndDirFmt: 'barcodes.fastq.gz'
I'm glad you got Qiime2 installed and running, and also found the Moving Pictures Tutorial.
As you have discovered, that tutorial shows one way to perform analysis. It's pretty linear.
As you have also discovered, there are lots of data types so there has to be different ways to process them. Check out the Importing data page, and replace that section in the Moving Pictures Tutorial with the section that matches your data!
(Let us know if you have any questions about how to do this.)
P.S. If you want to learn more...
Then check out this page that shows all the ways you can import then process your raw data using Qiime2!
Thank you Colin. This is helpful. I can import my data now. It is a multiplexed single end barcode in sequence file. The next step is demuxiplex using cutadapt.
I tried to use the code
qiime cutadapt demux-single \
--i-seqs multiplexed-seqs.qza \
--m-barcodes-file sample_metadata.tsv \
--m-barcodes-column barcode_sequence \
--p-minimum-length 120 \
--o-per-sample-sequences DEMUX_SEQS.qza \
--o-untrimmed-sequences UNMATCHED_SEQS.qza
but I dont have barcodes file. Can you suggest me what should I do next?
I know which sample match which barcode but it just that the files are not in the format required by qiime. Also, I got to know that dada2 for pacBio products are not supported by qiime2. So, I have to process them in R.
