Hi all,
I just got my MiSeq data for fungal ITS sequences in a large number of samples. I am going to be using QIIME to do the analysis and I have a basic workflow from another person, but I wasn't sure about where paired end assembly would be in the workflow.
I know that MiSeq data is already demultiplexed and that I will be using the split_libraries_fastq.py function, but do I need to do paired end assembly before that? What program is best to use for that, PANDASeq or join_paired_ends.py? For each sample I have two FASTQ files, Read 1 and Read 2, but the workflow I have does not address that.
Thanks
I just got my MiSeq data for fungal ITS sequences in a large number of samples. I am going to be using QIIME to do the analysis and I have a basic workflow from another person, but I wasn't sure about where paired end assembly would be in the workflow.
I know that MiSeq data is already demultiplexed and that I will be using the split_libraries_fastq.py function, but do I need to do paired end assembly before that? What program is best to use for that, PANDASeq or join_paired_ends.py? For each sample I have two FASTQ files, Read 1 and Read 2, but the workflow I have does not address that.
Thanks
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