Lennert van Overbeeke

icon indicating a website link https://nl.linkedin.com/in/lennertvo

icon company WFSR icon location Renkum icon location Food Safety & Bioinformatics with Python (also a little bit of PHP with Laravel)

Results 3 issues of Lennert van Overbeeke

Increase k-mer size above 31

3 comment

Hi, After finding some relevant consecutive 31-mers, we would like to repeat the workflow with k=41 in order to focus our search. The template config.yaml discourages this, and it becomes...

Questionable FASTQ format in test dataset

Hi, I ran into an error doing the test: ``` Started analysis of individual_99_R1.fastq Failed to process file individual_99_R1.fastq uk.ac.babraham.FastQC.Sequence.SequenceFormatException: Midline 'CCCFFFFFHHHHHJJJHGIJJJIJJGJGIJJJJIGIJJJIJJIFHGIIJIGJJFHEHI=DGGEEHHFFDFFFDEDEEDDBDBEFEEEEDDDDDDDDDDDDDDBDDDDDDCDDDDDDDDDDDDDADDDDDDBDDDDDDDCDDDDEDDEDEDE' didn't start with '+' at uk.ac.babraham.FastQC.Sequence.FastQFile.readNext(FastQFile.java:172) at uk.ac.babraham.FastQC.Sequence.FastQFile.next(FastQFile.java:125)...

How to read `results/kmers_count/<sample>/kmers_with_strand` table

Hi, I'd like to do some custom k-mer presence analyses on a per-sample basis. I'd like to read the individual k-mer databases per sample (`results/kmers_count//kmers_with_strand`), but the only files left...