hi,
I m using QIIME for OTU identification.
I have raw paired fastq files.
i do not have any information of barcode and linker primer .So i decided to create a barcode file using extract_barcodes.py script. this command run sucessfully and as a result i got three files read1.fastq resd2.fastq and barcodes.fastq.
command i used is --
extract_barcodes.py --input_type barcode_paired_end -f CIM_R1.fastq -r CIM_R2.fastq --bc1_len 6 --bc2_len 8 -o parsed_barcodes/
my query is ---
what is meaning of this --bc1_len 6 and --bc2_len 8 ? Its seems to be a length of barcode but how can i decide this is perfect lenght for my raw data.
Now, how can i use these file in split_libraries.py script. i read the tutorial but i am not able to understand.
can we run the whole process without having information of barcode and linkerprimer.?
hi, I m using QIIME for OTU identification. I have raw paired fastq files.
i do not have any information of barcode and linker primer .So i decided to create a barcode file using extract_barcodes.py script. this command run sucessfully and as a result i got three files read1.fastq resd2.fastq and barcodes.fastq.
command i used is -- extract_barcodes.py --input_type barcode_paired_end -f CIM_R1.fastq -r CIM_R2.fastq --bc1_len 6 --bc2_len 8 -o parsed_barcodes/
my query is ---