Hi! new Qiime2 user here!
I've been dealing with an issue in the demultiplexing step. I'm trying to repeat an analysis of a previously published paper. I've got their forward and reverse fastq files, barcodes, and metadata. after demuxing and getting the summary table, the read count for each sample is extremely low(max 43000, min 73 !).
I've checked different flags( also –p-golay-error-correction-details ), and the script pasted below is the only way that I even get an output :
What is the output when you run gunzip -c <file> | wc -l on either the forward or reverse reads file? This (divided by four) will tell you how many demultiplexed reads you would expect in the best case.
Hi @colinvwood
the command gives "62479544" back to me. also in the paper they state that they get > median depth of sequencing of 12,385 reads per sample (IQR = 10840-16136). there are 100 samples
the details file was too large to upload here but here is the link to google drive:
Providing both the --p-rev-comp-barcodes flag and the --p-rev-comp-mapping-barcodes flag at the same time should have the same effect as providing neither. Have you tried just one or the other?