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We discovered inconsistencies in kmer histograms on two experimental ONT datasets between uncompressed and compressed FASTA input files*. In independent runs and testing different k values (16,18,20,22,25), two gzipped FASTA ONT (NA19240 [PRJEB29523] and NA12878 [SRR10965087]) read files yielded jagged and uninterpretable kmer profiles. Problem exacerbated at higher k vals. Issue observed with ntcard v1.1.1, v1.2.1 and v1.2.2.
NA12878 ONT FASTA
NA12878 ONT FASTA GZIPPED
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NA19240 ONT FASTA
NA19240 ONT FASTA GZIPPED
*We have only observed this with FASTA files, not FASTQ files and only when using experimental nanopore data
The text was updated successfully, but these errors were encountered:
We discovered inconsistencies in kmer histograms on two experimental ONT datasets between uncompressed and compressed FASTA input files*. In independent runs and testing different k values (16,18,20,22,25), two gzipped FASTA ONT (NA19240 [PRJEB29523] and NA12878 [SRR10965087]) read files yielded jagged and uninterpretable kmer profiles. Problem exacerbated at higher k vals. Issue observed with ntcard v1.1.1, v1.2.1 and v1.2.2.
NA12878 ONT FASTA
![HG12878_FASTAlog10](https://user-images.githubusercontent.com/5719157/102518805-9795d700-4046-11eb-9879-e951de651606.png)
NA12878 ONT FASTA GZIPPED
![HG12878_GZFASTA_log10](https://user-images.githubusercontent.com/5719157/102518720-7cc36280-4046-11eb-94e8-81498bcb9291.png)
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NA19240 ONT FASTA
![NA19240log10FASTAuncompressed](https://user-images.githubusercontent.com/5719157/102524066-4ccb8d80-404d-11eb-8bfb-e2cc3e69b0c7.png)
NA19240 ONT FASTA GZIPPED
![NA19240log10FASTAcompressed](https://user-images.githubusercontent.com/5719157/102524083-535a0500-404d-11eb-8005-dd23814554d2.png)
*We have only observed this with FASTA files, not FASTQ files and only when using experimental nanopore data
The text was updated successfully, but these errors were encountered: