I just don't know what's the meaning of it.
Is there anyone explain it for me ?
Thanks !XD
Is there anyone explain it for me ?
Thanks !XD
-
-
I am not sure about IDBA, but Tadpole has a seed kmer flag, and the meaning is:
Contigs are built starting with a single kmer, then extending it. However, only kmers with a sufficiently high count (number of times they are observed in reads) are used as seeds, because kmers with a very low count are likely to be erroneous. So Tadpole's default "mincountseed=3" ensures that no contig will ever be created that does not have at least one kmer in it with a depth of at least 3. I suspect IDBA uses a similar mechanism. -
Thank you .Originally posted by Brian Bushnell View Post
But as idba_ud has a parameter '--min count' with description 'minimum multiplicity for filtering k-mer when building the graph', I guess maybe what you say is something like this.[?]
Sorry that I forgot to write down the description of seed kmer, 'seed kmer size for alignment'。 But I really can't understand. Is it means when constructing the graph, the first kmer needs to be this size[seed kmer] and other kmers' length will be the sum of mink and step?Comment
-
Oh... in that case, speculation again, but it sounds like it is for a scaffolding phase; essentially, a match of at least that long is required in a read to consider it as having come from that scaffold.Comment
-
CRISPR/Cas9 sparked the gene editing revolution for both research and therapeutics.1 But this system still showed severe issues that limited its applications. The most prominent were the heavy reliance on PAM sequences, delivery limitations, double-stranded breaks that prompt unintended edits and cell death, and editing inefficiency (both in targeting and in knock-in reliability).
Despite this, “CRISPR helped turn genome editing from a specialized technique into...Yesterday, 11:01 AM -
Proteomics platforms are evolving rapidly, with advances in mass spectrometry and affinity-based approaches expanding what researchers can detect and at what scale. As the field moves toward deeper proteome coverage and clinical applications, scientists face an increasingly complex landscape of tools. This article will explore how researchers are navigating these choices to find the right platform for their work.
The systematic characterization of the human proteome has...07-20-2026, 11:48 AM -
Genomics studies in neuroscience face a special challenge due to the brain’s complexity and scarcity of samples. Mapping changes in cell type and state using conventional next-generation sequencing methods remains challenging. Advances in technologies like single-cell sequencing, spatial transcriptomics, and long-read sequencing have opened the door to deeper studies of the brain and diseases like Alzheimer’s, amyotrophic lateral sclerosis (ALS), and schizophrenia.
...07-09-2026, 11:10 AM
Comment