How can sequence with lower-case masking be converted to unmasked sequence?.How do alignment programs treat the lower-case masking in genomic fasta files?.Are repetitive sequences in eukaryotic genomes masked?.Do you provide assembly data formatted for use by sequence read alignment pipelines?.Why do some species directory names start with an underscore?.Why was the sequence identifier format in the FASTA files changed?.How can I download all genome assemblies from the Human Microbiome Project, or other project?.How can I download RefSeq data for all complete bacterial genomes?.How can I download only the current version of each assembly?.Where can I find information to help me chose between the many different assemblies for a species?.How can I find the sequence and annotation of my genome of interest?.What is the content of annotation_releases in the refseq directory hierarchy?.What additional files are provided for RefSeq genomes annotatated by the NCBI Eukaryotic Genome Annotation Pipeline?.What is the file content within each specific assembly directory?.How are the FTP directories structured?.Is the genome the same? Which one should I use? My organism of interest is available in both GenBank and RefSeq.Are files on the FTP site updated following annotation updates?.Are all genomes available in NCBI nucleotide available on the FTP site?.How can I stay informed about changes to the NCBI genomes FTP site?.Why was the NCBI genomes FTP site reorganized?.What is the best protocol to use to download large data sets?.What is the easiest way to download data for multiple genome assemblies?.What are the highlights of the genomes FTP site?.
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