human genome h38 infromation downloading

Writing date: 2015-11-17.

The latest Human Genome assembly version is : GRCh38 (GCA_000001405.15) . GRch38: Genome Reference Consortium Human Reference 38.

The GRch38 genome browses:
UCSC http://genome.ucsc.edu/cgi-bin/hgGateway
Ensembl http://www.ensembl.org/Homo_sapiens/Info/Index
Vega http://vega.sanger.ac.uk/Homo_sapiens/Info/Index
GENCODE http://www.gencodegenes.org/human_biodalliance.html

The downloading website of GRch38 information in Ensembl: http://www.ensembl.org/info/data/ftp/index.html
I recommend to download gh38 sequence functional annotations from Ensembl: ftp://ftp.ensembl.org/pub/release-82/genbank/homo_sapiens/.

mdkir sequence_annotation
cd sequence_annotation
lftp -e "mirror -c --parallel=5 /pub/release-82/genbank/homo_sapiens/" ftp://ftp.ensembl.org
cd ..

The downloading website of GRch38 information in GENCODE: http://www.gencodegenes.org/releases/23.html
I recommend to download gh38 fasta and gff3 files from GENCODE. These 2 files would be the main fasta and gff3 files for most users.

wget ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_23/GRCh38.primary_assembly.genome.fa.gz
wget ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_23/gencode.v23.basic.annotation.gff3.gz

SVG更改坐标系原点位置

在使用FigTree画树后。由于设置字体大小>14,于是导致export出来的图片中最上面一行字被截断了,从而使图片很丑。于是export出SVG格式文件。然后修改SVG坐标系原点位置,将图片完整显示出来。

在 <svg xmlns… 这行尾部添加 transform=”translate(0,20)”  width=”xxx” height=”xxx”解决。