注释有很多版本，比如ensembl，gencode, ucsc known gene, NCBI的RefSeqGene。最近就需要NM id的注释，但NCBI提供的是gff3格式的，而且很乱。用UCSC table browser下载的gtf版本的RefSeq，没有转录本和基因之间的关系，也没有基因symbol。
比如Ensembl，其实Ensembl的gtf挺好用的，不过这次我因为需要NM编号的注释（笨方法是将ensembl id转成NCBI的refSeq的ID，但这不是最优的方法，ID mapping有可能对不上，不如直接用NM的注释）。
1
2
3
|
chr1 ensembl_havana gene 11869 14412 . + . gene_id "ENSG00000223972"; gene_version "4"; gene_name "DDX11L1"; gene_source "ensembl_havana"; gene_biotype "pseudogene";
chr1 havana transcript 11869 14409 . + . gene_id "ENSG00000223972"; gene_version "4"; transcript_id "ENST00000456328"; transcript_version "2"; gene_name "DDX11L1"; gene_source "ensembl_havana"; gene_biotype "pseudogene"; transcript_name "DDX11L1-002"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTHUMT00000362751"; havana_transcript_version "1"; tag "basic";
chr1 havana exon 11869 12227 . + . gene_id "ENSG00000223972"; gene_version "4"; transcript_id "ENST00000456328"; transcript_version "2"; exon_number "1"; gene_name "DDX11L1"; gene_source "ensembl_havana"; gene_biotype "pseudogene"; transcript_name "DDX11L1-002"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTHUMT00000362751"; havana_transcript_version "1"; exon_id "ENSE00002234944"; exon_version "1"; tag "basic";
|
UCSC table browser下载的refGene的gtf，这个文件不对的地方是gene id和transcript id是一个，而我需要gene和transcript的关系
1
2
3
4
5
6
|
chr1 hg19_refGene exon 66999276 66999355 0.000000 + . gene_id "NM_001308203"; transcript_id "NM_001308203";
chr1 hg19_refGene start_codon 67000042 67000044 0.000000 + . gene_id "NM_001308203"; transcript_id "NM_001308203";
chr1 hg19_refGene CDS 67000042 67000051 0.000000 + 0 gene_id "NM_001308203"; transcript_id "NM_001308203";
chr1 hg19_refGene exon 66999929 67000051 0.000000 + . gene_id "NM_001308203"; transcript_id "NM_001308203";
chr1 hg19_refGene CDS 67091530 67091593 0.000000 + 2 gene_id "NM_001308203"; transcript_id "NM_001308203";
chr1 hg19_refGene exon 67091530 67091593 0.000000 + . gene_id "NM_001308203"; transcript_id "NM_001308203";
|
中间找了很多，终于找到一个方法，https://bioinformatics.stackexchange.com/questions/2548/hg38-gtf-file-with-refseq-annotations
mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -N -e "select * from refGene" hg19 ' cut -f2- ' genePredToGtf -source=hg19.refGene.ucsc file stdin stdout > refSeq.hg19.gtf
genePredToGtf可以从UCSC下载，需要注意的直接下载refFlat的文件（不通过mysql），用genePhredToGtf生成的文件和UCSC table browser下载的gtf文件是一样的，通过mysql下载用genephreadToGtf是我想要的。
比如这样，这才是我想要的
1
2
3
4
|
chrX hg19.refGene.ucsc exon 70683674 70685855 . + . gene_id "TAF1"; transcript_id "NM_138923"; exon_number "38"; exon_id "NM_138923.38"; gene_name "TAF1";
chrX hg19.refGene.ucsc CDS 70683674 70683893 . + 1 gene_id "TAF1"; transcript_id "NM_138923"; exon_number "38"; exon_id "NM_138923.38"; gene_name "TAF1";
chrX hg19.refGene.ucsc start_codon 70586225 70586227 . + 0 gene_id "TAF1"; transcript_id "NM_138923"; exon_number "1"; exon_id "NM_138923.1"; gene_name "TAF1";
chrX hg19.refGene.ucsc stop_codon 70683894 70683896 . + 0 gene_id "TAF1"; transcript_id "NM_138923"; exon_number "38"; exon_id "NM_138923.38"; gene_name "TAF1";
|
Ref: https://bioinformatics.stackexchange.com/questions/2548/hg38-gtf-file-with-refseq-annotations
####################################################################
#版权所有 转载请告知 版权归作者所有 如有侵权 一经发现 必将追究其法律责任
#Author: Jason
####################################################################
