-
Notifications
You must be signed in to change notification settings - Fork 9
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Jagged kmer coverage profiles with gzipped FASTA #46
Comments
Might be due to streaming in compressed multiline/single-line fasta records. Can you give this a try with ntCard v1.1.1? |
yes, "Issue observed with ntcard v1.1.1, v1.2.1 and v1.2.2" |
thanks. will investigate this. |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
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
====
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: