...DERATE or LOW impact).GENEGene name (usually HUGO)GENEIDGene ID)FEATUREThetypeof feature is in the next field (e.g. transcript, motif, miRNA, etc.)FEATUREIDTranscript ID (preferably using version number), Motif ID, miRNA, ChipSeq peak, Histone mark, depending on the annotation.BIOTYPEDescription o...
... -format => 'fasta');while ( my $seqobj = $in->next_seq() ) {
# the human read-able id ofthe sequence
my $id=$seqobj->id(); # string of sequence
my $seq=$seqobj->seq();
# a description ofthe sequence
my $desc=$seqobj->desc();
# one of 'dna','rna','protein' https://www.bi...
...message and exit
-i maffile, --maf maffile
input the maf file[required]
-m metadata, --meta metadata
input metadata file path[required]
-g group, --group group
input group id in metadata file to classification
...
...可以做的分析：
Indentify unique SNPs profiles and assign sequence types(MST);Calculate allele frequencies;Find informative SNPs;Calculate D (Index ofthe Discrininatory Ability);Find the set(s) of minimum SNPs;Output MST data file in mega and interleaved mega format.
输入的文件格式...
...vironment value of R_HOME
--> Q&A for bioinformatics, please visit the website: https://www.omicsclass.com/
--> R beginners ? I suggest your learning R language: https://study.omicsclass.com/index
Registered S3 methods overwritten by 'treeio':
method from
...
...[File Out]stdout -F过滤询问序列[String]TDUST with blastn, SEG with others-G打开gap得分[Integer]-1 -E延伸gap得分[Integer]-1 -XX dropoff value for gapped alignment (in bits)[Integer]0blastn 30, megablast 20, tblastx 0, all others 15-I显示gi号Show GI’s in deflines[T/F]F -q核酸...
...if a requested column cannot be found instead of just skipping the data set [default: FALSE] -b NAME, --background=NAME Column to define the background colours ofthe tip labels; empty means no background colours [default:...
...信息，如： population frequency in different populations 和various types of variant-deleteriousness prediction scores，这些可被用来过滤掉一些公共的及 probably（大概，肯定的成分较大,，是most likely）nondeleterious variants。
一、基于基因的注释（gene-...
...d exit
-g GENE_DATA, --gene_data GENE_DATA
Enter the file path that contains the gene symbol and
gene grouping[required]
-p P_DATA, --p_data P_DATA
input data file path[required]
-r R_DATA, --r_data R_DATA
...