Chimeric reads identification and removal
I am thinking to use "identify_chimeric_seqs.py" from QIIME package (method - blast_fragments) for chimeric reads removal.
Can someone let me know where can I find the input files?
identify_chimeric_seqs.py -i repr_set_seqs.fasta -t taxonomy_assignment.txt -r ref_seq_set.fna -m blast_fragments -o chimeric_seqs_blast.txt
Where can I find below files?:
repr_set_seqs.fasta taxonomy_assignment.txt ref_seq_set.fna chimeric_seqs_blast.txt
I have paired end 16s rRNA data (QC checked, trimmed and stiched using FLASH).
Thanks
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You can get from the script split_library_fastq
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