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6
votes
2answers
709 views

How can I edit a specific FASTQ read in place, given the read ID?

Given a read ID, I want to edit a single basecall (e.g. the 12th base) for just that read from within a large FASTQ file containing millions of reads. example, i want to change the 12th base ('C') in ...
9
votes
2answers
2k views

How do you generate read-length vs read-quality plot for long-read sequencing data (e.g., MinION)?

How do you generate read-length vs read-quality plot (heat map with histograms in the margin) for long-read sequencing data from the Oxford Nanopore Technologies (ONT) MinION? The MinKNOW software ...
6
votes
1answer
851 views

How to maximize fastq parsing with FastqGeneralIterator (Bio.SeqIO.QualityIO)

I'm contributing to a python-based project that uses Biopython to analyze fastq files. It currently uses SeqIO.parse, which ...