# 转录组入门（4）：了解参考基因组及基因注释

• A+

## 准备工作

### 参考基因组

UCSC网站

hg19

chromFa.tar.gz - The assembly sequence in one file per chromosome.Repeats from RepeatMasker and Tandem Repeats Finder (with period of 12 or less) are shown in lower case; non-repeating sequence is shown in upper case.

cd /mnt/f/Data
mkdir reference && cd reference
mkdir -p genome/hg19 && cd genome/hg19
tar -zvf chromFa.tar.gz
cat *.fa > hg19.fa
rm chr*

### 注释信息

Gencode

GTF/GFF3

GTF（General Transfer Format）其实就是GFF2，以Tab分割，分为如下几列

1. seqname - name of the chromosome or scaffold; chromosome names can be given with or without the 'chr' prefix. Important note: the seqname must be one used within Ensembl, i.e. a standard chromosome name or an Ensembl identifier such as a scaffold ID, without any additional content such as species or assembly. See the example GFF output below.
2. source - name of the program that generated this feature, or the data source (database or project name)
3. feature - feature type name, e.g. Gene, Variation, Similarity
4. start - Start position of the feature, with sequence numbering starting at 1.
5. end - End position of the feature, with sequence numbering starting at 1.
6. score - A floating point value.
7. strand - defined as + (forward) or - (reverse).
8. frame - One of '0', '1' or '2'. '0' indicates that the first base of the feature is the first base of a codon, '1' that the second base is the first base of a codon, and so on..
9. attribute - A semicolon-separated list of tag-value pairs, providing additional information about each feature.

1. seqid - name of the chromosome or scaffold; chromosome names can be given with or without the 'chr' prefix. Important note: the seq ID must be one used within Ensembl, i.e. a standard chromosome name or an Ensembl identifier such as a scaffold ID, without any additional content such as species or assembly. See the example GFF output below.
2. source - name of the program that generated this feature, or the data source (database or project name)
3. type - type of feature. Must be a term or accession from the SOFA sequence ontology
4. start - Start position of the feature, with sequence numbering starting at 1.
5. end - End position of the feature, with sequence numbering starting at 1.
6. score - A floating point value.
7. strand - defined as + (forward) or - (reverse).
8. phase - One of '0', '1' or '2'. '0' indicates that the first base of the feature is the first base of a codon, '1' that the second base is the first base of a codon, and so on..
9. attributes - A semicolon-separated list of tag-value pairs, providing additional information about each feature. Some of these tags are predefined, e.g. ID, Name, Alias, Parent - see the GFF documentation for more details.

nohup wget ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_26/GRCh37_mapping/gencode.v26lift37.annotation.gtf.gz &
nohuop wget ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_26/GRCh37_mapping/gencode.v26lift37.annotation.gff3.gz &


### IGV， Integrative Genomics Viewer

Windows下载如下版本， 会自带一个java运行环境

sort

gene演示

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转录组入门（4）：了解参考基因组及基因注释