BED output file指定输出文件的名字,如果不指定,默认会显示在浏览器中共,如果下载整个基因组的信息,建议填写输出文件的名字,file type returned选择返回文件的格式,支持返回压缩文件。 通过简单的勾选,就可以下载到GTF文件了。但是这种方式下载的GTF文件是有限制的,只包含了转录本ID, 示例如下 代码语言:javascript 代码...
tblastn -query proteins.fa -db target_genome.fa -num_threads 16 -outfmt 6 > prots_vs_genome.tab Run blast2gff.py on the output file. This will reformat the tabular blast hits into gff3 alignment style. Simple filtering options can be applied with-e-sand-F. If the queries were from ...
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选好了基因组,gtf/gff3的问题也迎刃而解——选择对应的版本就好了。 .gtf: 默认文件,对应primary assembly.fa(This is the default file, it should contain the full annotation for all species except human and mouse. For human and mouse, it will contain all annotation on the primary assembly, ie ...
args=parser.parse_args()defget_id(id_list,id_from,trans_to):withopen(args.gtf,'r')asgff:result=[]hash_dict=dict()forlineingff:line1=line.strip().split('\t',8)try:Name=line1[8]except:continuetry:from_type=eval(Name.split(id_from)[1].split(';')[0])#hash methods, it need...
tblastn -query proteins.fa -db target_genome.fa -num_threads 16 -outfmt 6 > prots_vs_genome.tab Run blast2gff.py on the output file. This will reformat the tabular blast hits into gff3 alignment style. Simple filtering options can be applied with-e-sand-F. If the queries were from ...