Hello all and sorry if this is in the wrong area. I’m trying to get individual FASTQ files for each sample from the large output file after a MiSeq run. The plan was to use QIIME 1, run the split_libaries_fastq.py script on the forward and reverse fastq files separately, then run the extract_seq_by_sample_id.py to create the separated fastq files. However, I’m running into a few issue. First, I get an error stating some or all bacodes are not golay if I run:
split_libraries_fastq.py
-i reverse.fastq
-o split_libraries_reverse
-b barcodes_fixedheaders.fastq
-m Sponge_mapping_corrected_corrected.txt
–store_demultiplexed_fastq \
I then added “–rev_comp_mapping_barcodes” to the end and that seemed to fix the issue, or at least generate a seqs.fastq file. When I then go to run extract_seq_by_sample_id.py, I get an error “AttributeError: ‘NoneType’ object has no attribute ‘strip’”
Not sure if there is some modification I need to do to these commands since I’m running a forward and reverse separately instead of joining them, or if there is even a better way to do this. Any help would be greatly appreciated.