Hello,
I am new to qiime2 and trying to analyze my data, but stack at the step of analyzing the quality of reads. Below I quickly indicated what I did so far,
1- I have two fastq-files (forward and reverse) and had to run “bcl2fastq” to demultiplexing because index.fatq file was not provided/generated.
2- I had run qiime import using a manifest file
"~$ qiime tools import --type SampleData[PairedEndSequencesWithQuality] --input-path pilot-manifest --output-path paired-end-demux.qza --source-format PairedEndFastqManifestPhred33"
It did work and I got my paired-end-demux.qza file
3- to analyze the read and visualize them, I had run
" ~$ qiime demux summarize --i-data paired-end-demux.qza --o-visualization demux.qzv"
This step did also work, but I could not know how many reads per barcodes I do have out of the sequencing as indicated in the tutorial Atacama. Is there a way to do that ? Many Thanks for the help
Thanks for the great summary of what you have done so far, that was really helpful!
If I am understanding the question correctly, that info should be found in your demux summarize viz, take a look at the bottom of the first page in that viz (example from the atacama tutorial):
The first column lists your Sample ID, and the second is the number of reads in that sample. Your samples map one-to-one to your barcodes, so you could download that CSV listed at the bottom of the table and add another column with your barcodes, if you wanted. In QIIME 2, barcodes are only used right now as part of the demultiplexing process, so I'm not really sure what this activity would buy you, but please let me know if you have a particular need in mind!
My issue is I do not have a list of barcodes/sample name with corresponding read number. Instead, I have sample 1 with all read of the MiSeq run. I attached my screen
I also provide below my manifest file text,
sample-id,absolute-filepath,direction
sample1,$PWD/emp-paired-end-sequences/forward_reads.fastq,forward
sample1,$PWD/emp-paired-end-sequences/reverse_reads.fastq,reverse
I understand that the viz can not provide stat for each sample name, because I did not provide so far. However, I do not see at which step I could do it, since I have this particular case of importing data with manifest.
I hope these info make it clearer!
Oops! You mention above that you had already demultiplexed your data:
But from your screenshot, it looks like the data you imported is not demultiplexed.
If you are already running bcl2fastq, it might be easiest for you to demultiplex your data with that tool, and then import the resulting demultiplexed files into QIIME 2 using a manifest format.
We are also working on implementing a q2-cutadapt plugin, which will support demultiplexing paired end data that have barcodes still in the forward reads, so you could also wait for that to land (theoretically in the upcoming 2017.12 release).
