-
The `tetra-freq` module crashes if there is an `N` nucleotide in the nucleotide sequence.
An example error message is:
> File "/home/ubuntu/.local/lib/python3.6/site-packages/magpurify/modules/t…
-
Kallisto seems to detect a large number of non-ACGUT characters when none exist. When I try to create an index using kallisto index, this is part of the output:
[build] warning: replaced 5334758 non…
-
When using 30X hifi data, 0.16.1-r375 with default parameter produce a larger assembly fasta(the Genome size is estimated to be 2.2G, assembly result is 3.0G).Compared with the kmer distribution of an…
-
Given a (minimum and) maximum read length, and a PRG,we should be able to
1. decide that there are some places we will never be able to draw inference on, so we might as well ignore (which means d…
-
Hi,
To preface this, I know this is not a standard use case, so I'm not expecting there to be a happy resolution.
I've been trying to test how low the coverage can go to see which metrics (auN, as…
-
Hi,
I am using SeqAn 2.3.2. I am following sequence I/O tutorial. The steps mentioned to read records in chunks is not very much clear. For example, I have a fastq file with 100 records. I am tryin…
-
Hi,
I received an error when attempting to perform krakenuniq-build on the refseq genomes.
This is the command I use:
./scripts/krakenuniq-build --db DBDIR-temp --kmer-len 31 --threads 10 --…
-
Hi!!
MAX_KMER_SIZE: The maximum k-mer size is set to 64, but can it be changed from default 31?"
If it is possible, please provide detailed instructions.
Thank you!!
-
I don't know if you're interested, but there's a much easier way of doing Smith-Waterman that involves having an extra row and column at the 0th indexes, whose scores are all zero. You only need a sin…
mmcco updated
9 years ago
-
Hi,
I have been unable to call the add operation more than once. The first time is successful, but then on the second call, it fails. E.g.
java -Xmx8g -jar /home/matt/pantools/dist/pantools.jar…