MCScanX gene id 问题

作者: 溪溪溪溪溪川 | 来源:发表于2021-03-15 16:25 被阅读0次

MCScanX gene id 问题
【跟着manual学软件】MCScan-transposed
基因ID类型
gene ID / Gene Symbol / Ensembl
2021-04-08 探针与基因id的转换
Gene ID转换
R中如何将ENSEMBL ID转换成Gene ID(ENTREZ
RNA-seq分析（四）pathway analysis
基因ID之间的自由切换
Kobas数据库使用介绍

该gff 的gene行存在Name，导致脚本没有考虑到这种情况，提取的gene id为Name，gene id 过长，导致MCScanX无法运行。
解决方法：将第九列去掉Name既可。

awk -F '[\t;]' '{if($3~/gene/) {print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9";} else{print $0}}'  Dod.chr.gff3 
chr07   .   gene    28275981    28288196    .   -   .   ID=evm.TU.scaffold_30.17;
chr07   .   mRNA    28275981    28288196    .   -   .   ID=evm.model.scaffold_30.17;Parent=evm.TU.scaffold_30.17;Name=EVM%20prediction%20scaffold_30.17
chr07   .   five_prime_UTR  28288064    28288196    .   -   .   ID=evm.model.scaffold_30.17.utr5p1;Parent=evm.model.scaffold_30.17
chr07   .   five_prime_UTR  28287389    28287395    .   -   .   ID=evm.model.scaffold_30.17.utr5p2;Parent=evm.model.scaffold_30.17
chr07   .   exon    28288064    28288196    .   -   .   ID=evm.model.scaffold_30.17.exon1;Parent=evm.model.scaffold_30.17
chr07   .   exon    28287253    28287395    .   -   .   ID=evm.model.scaffold_30.17.exon2;Parent=evm.model.scaffold_30.17
chr07   .   CDS 28287253    28287388    .   -   0   ID=cds.evm.model.scaffold_30.17;Parent=evm.model.scaffold_30.17
chr07   .   exon    28281681    28282520    .   -   .   ID=evm.model.scaffold_30.17.exon3;Parent=evm.model.scaffold_30.17

chr07   .   gene    28275981    28288196    .   -   .   ID=evm.TU.scaffold_30.17;Name=EVM%20prediction%20scaffold_30.17
chr07   .   mRNA    28275981    28288196    .   -   .   ID=evm.model.scaffold_30.17;Parent=evm.TU.scaffold_30.17;Name=EVM%20prediction%20scaffold_30.17
chr07   .   five_prime_UTR  28288064    28288196    .   -   .   ID=evm.model.scaffold_30.17.utr5p1;Parent=evm.model.scaffold_30.17
chr07   .   five_prime_UTR  28287389    28287395    .   -   .   ID=evm.model.scaffold_30.17.utr5p2;Parent=evm.model.scaffold_30.17
chr07   .   exon    28288064    28288196    .   -   .   ID=evm.model.scaffold_30.17.exon1;Parent=evm.model.scaffold_30.17
chr07   .   exon    28287253    28287395    .   -   .   ID=evm.model.scaffold_30.17.exon2;Parent=evm.model.scaffold_30.17
chr07   .   CDS 28287253    28287388    .   -   0   ID=cds.evm.model.scaffold_30.17;Parent=evm.model.scaffold_30.17
chr07   .   exon    28281681    28282520    .   -   .   ID=evm.model.scaffold_30.17.exo

LIU_sa07    EVM20prediction20scaffold_30.17 28275981    28288196
LIU_sa07    EVM20prediction20scaffold_30.1  27505683    27508995
LIU_sa07    EVM20prediction20scaffold_30.33 28962370    28967589
LIU_sa07    EVM20prediction20scaffold_30.74 29946477    29988627
LIU_sa07    EVM20prediction20scaffold_30.62 29734064    29735281