Chimeric reads identification and removal
1
0
Entering edit mode
5.4 years ago

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

qiime chimera • 1.8k views
ADD COMMENT
0
Entering edit mode
5.4 years ago
Picasa ▴ 610

You can get from the script split_library_fastq

ADD COMMENT

Login before adding your answer.

Traffic: 1426 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6