Kristian Ullrich
Kristian Ullrich
Dear Mattermost, after upgrading from Ubuntu16 to Ubuntu20 and after the OS upgrade from Mattermost v5.37 to 7.0.1 we still have some problems with the sql. The first problem was:...
Hi, according to the manual at the moment, the reverse complement and in case of is_protein=True all 6 possible open reading frames are considered. Is there an option to keep...
Hi, are there any recommandation for eukaryotic species? I am currently comparing two highly similar eukaryotic genome sequences, but get no synteny nor any rearrangements at all? ``` wget http://ftp.ensembl.org/pub/current_fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz...
minimap2
Hi, is SNPsplit incompatible to minimap2, as it is mentioned that bwa is not compatible? Thank you in anticipation Best regards Kristian
Hi, I am using angsd to produce fasta sequences, these are automatically gzipped fasta files. If I open the fasta file with R-Biostrings the sequence compositon looks like this: ```...
Dear @alekseyzimin, I was wondering if it would be possible to add an option to completely turn off query scaffold splitting if one chooses to use the `-nb` option. The...
Dear sourmash-bio team, this is a feature request. Unlike nt-genomes I am comparing protein based minhashes. Here, every single protein of one species and its corresponding minhash is compared to...
Dear David Emms, next to BLAST+, DIAMOND and MMSEQS2, LAST (https://gitlab.com/mcfrith/last) is another protein search alternative. It is known, that in comparison to diamond or mmseqs2 it lacks sensitivity but...
Dear samtools, I am working with FASTA alignments, which have different sequence names (aka chromosomes) but all of the same length. No I needed to create a wrapper around samtools...
Hi, I have encountered that the sequence order for the processed sequences differ from the original input fasta file. Is it possible to retain the order directly with pre-msa.bf? Thank...