bedtools如何统计序列中碱基含量

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bedtools统计序列中碱基含量

bedtools软件中的nuc函数工具可以统计序列碱基含量，其具体用法如下：

Tool:    bedtools nuc (aka nucBed)Version: v2.25.0Summary: Profiles the nucleotide content of intervals in a fasta file.Usage:   bedtools nuc [OPTIONS] -fi  -bed Options:        -fi     Input FASTA file        -bed    BED/GFF/VCF file of ranges to extract from -fi        -s      Profile the sequence according to strand.        -seq    Print the extracted sequence        -pattern        Report the number of times a user-defined sequence                        is observed (case-sensitive).        -C      Ignore case when matching -pattern. By defaulty, case matters.        -fullHeader     Use full fasta header.                - By default, only the word before the first space or tab is used.Output format:        The following information will be reported after each BED entry:            1) %AT content            2) %GC content            3) Number of As observed            4) Number of Cs observed            5) Number of Gs observed            6) Number of Ts observed            7) Number of Ns observed            8) Number of other bases observed            9) The length of the explored sequence/interval.            10) The seq. extracted from the FASTA file. (opt., if -seq is used)            11) The number of times a user's pattern was observed.                (opt., if -pattern is used.)

示例如下：

bed文件：

CM004359.1      0       10CM004359.1      100     200CM004359.1      1000    1050

运行命令：

$bedtools nuc -fi GCA_001651475.1_Ler_Assembly_genomic.fna -bed id.bed#1_usercol      2_usercol       3_usercol       4_pct_at        5_pct_gc        6_num_A 7_num_C 8_num_G 9_num_T 10_num_N        11_num_oth      12_seq_lenCM004359.1      0       10      0.600000        0.400000        1       0       4       5       0       0       10CM004359.1      100     200     0.580000        0.420000        14      0       42      44      0       0       100CM004359.1      1000    1050    0.660000        0.340000        10      3       14      23      0       0       50

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