kmer extracting using quality
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Need first using "import module biopython" in MSU HPCC
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freq_dict is the file that I saved that contained a python dict object to chaek kmer frequency of all dataset, right now I only have 11mer one.
usage: python FastaProcess.py [-h] [-freq_dict DICT] [-freq FREQ] k template_fastq insertion_fastq output_fasta positional arguments: k length of kmer template_fastq the fastq file that contain sequence we want to extract kmer insertion_fastq the fastq file that contain insertion quality output_fasta the fasta file to store the extracted kmer optional arguments: -h, --help show this help message and exit -freq_dict DICT path that store frequency dict -freq FREQ the threshold to filter frequency
*use of bowtie2
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first need to build index on the referece file, here I used pair1_2.fasta as example (bowtie2 only take fasta, so every pair I should have at least one fasta file)
bowtie2-build XXX.fasta XXX_index_name -
bowtie2 command I used to generate 1 error for the kmer
bowtie2 -f -N 1 -L 6 -a -p 2 --score-min L,-0.8,-0.8 --norc -x index_path kmer_fasta_path -S sam_file_to_save_alignment