THE COLLECTION OF COMMON GENOME ANNOTATION
Genome GTF Rfam Structures RNAs Index Useful Softwares

Chain file

Chain files are used to covert genome version such as hg19=>hg38 and mm9=>mm10

Collected chain files are located in /150T/zhangqf/GenomeAnnotation/chain

Example: liftOver input.bed chainFile output.bed unmap.bed

File name Content
hg18ToHg19.over.chain.gz hg18 => hg19
hg18ToHg38.over.chain.gz hg18 => hg38
hg19ToHg17.over.chain.gz hg19 => hg17
hg19ToHg18.over.chain.gz hg19 => hg18
hg19ToHg38.over.chain.gz hg19 => hg38
hg38ToHg19.over.chain.gz hg38 => hg19
mm10ToMm9.over.chain.gz mm10 => mm9
mm9ToMm10.over.chain.gz mm9 => mm10

Size file

Size file record the size of each chromosome.

Size files are located in /150T/zhangqf/GenomeAnnotation/size

It can be produced when use STAR to build index (chrNameLength.txt)

chr1 248956422
chr2 242193529
chr3 198295559
chr4 190214555
chr5 181538259
chr6 170805979

Gene Description

The gene expression is from ensembl biomart

Directory: /150T/zhangqf/GenomeAnnotation/Gene_Description

ENSMUSG00000047631 Apof apolipoprotein F [Source:MGI Symbol;Acc:MGI:104539]
ENSMUSG00000079103 Tgm7 transglutaminase 7 [Source:MGI Symbol;Acc:MGI:2151164]
ENSMUSG00000038605 Samd10 sterile alpha motif domain containing 10 [Source:MGI Symbol;Acc:MGI:2443872]
ENSMUSG00000089917 Uckl1 uridine-cytidine kinase 1-like 1 [Source:MGI Symbol;Acc:MGI:1915806]
ENSMUSG00000074890 Lcmt2 leucine carboxyl methyltransferase 2 [Source:MGI Symbol;Acc:MGI:1353659]

Gene Ontology

The gene ontology is from geneontology database

Directory: /150T/zhangqf/GenomeAnnotation/Ontology