Open dgslos opened 1 year ago
Hi
Thank you for your interest in laca.
You need to analyze one amplicon each time. Just make sure the demultiplexed directories are named in a format of [a-zA-Z]+[0-9]+
. And the unzipped fastq files are put in each directory respectively.
demultiplexed_data1/
├─ sample1/
│ ├─ batch1.fastq
│ ├─ batch2.fastq
├─ sample2/
│ ├─ batch1.fastq
│ ├─ batch2.fastq
Best Yan
Hi,
I would like to analyse multiple samples at once after demultiplexing. As input data I have one fasta file for each sample and each amplicon.
I'm not sure how to organise my data and I could not find it in the documentation. So there are several options to organise the data:
Or
The wanted output file after clustering would be like this: clustered_consensus_all_samples_amplicon1.fasta clustered_consensus_all_samples_amplicon2.fasta
With corresponding count table for each amplicon like this:
Is laca currently able to produce output like this? And should I analyse one amplicon at a time or are multiple amplicons possible?
Thanks!