Hello,
I am using QIIME to analyse my sequencing data. I have used it before with Illumina data with no problems, but now I have Illumina MiSeq data and four raw data files: two index files and two raw reads files. I understand the raw reads files (one forward and one reverse that I can merge with join_paired_ends.py), but I do not know how to handle the two index files. How do I construct the mapping file with the two indexes? How do I use these index files as input for join_paired_ends.py and split_libraries_fastq.py? Should I use the extract_barcodes.py script before joining the paired end reads?
Thank you very much!
Hi please follow the description in http://qiime.org/tutorials/processing_illumina_data.html#two-index-barcode-reads-and-two-fastq-reads
example:
extract_barcodes.py --input_type barcode_paired_end -f index1.fastq -r index2.fastq --bc1_len 6 --bc2_len 6 -o parsed_barcodes/
I assume this is the one you need.
Best wishes,
Suparna
hi,
After using multiple_join_paired_ends.py, you can use multiple_split_libraries_fastq.py.
This script allow to run split_libraries_fastq.py on multiple demultiplexed files.
Hi Martha! Did you got some solution for that issue? I also don't know how to handle the two index files and how to construct the mapping file .... I recived two different mapping files. And I don't know how to deal with that.
Thanks a lot for your help!
I am having trouble in putting the mapping file specific to dual indexing what considerations have come up with?
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