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This article mainly shows you "how bedtools counts the base content in the sequence", which is easy to understand and clear. I hope it can help you solve your doubts. Let me lead you to study and learn this article "how to count the base content in bedtools sequence".

Base content in bedtools statistical sequence

The nuc function tool in bedtools software can count the base content of the sequence, and its specific usage is as follows:

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.)

Examples are as follows:

Bed file:

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

Run the command:

$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 04 500 10CM004359.1 100200 0.580000 0.420000 14 0 42 44 00 100CM004359.1 1000 1050 0.660000 10 3 14 23 00 50 and above is "how does bedtools count the order?" All the contents of the article "Base content in the column" Thank you for reading! I believe we all have a certain understanding, hope to share the content to help you, if you want to learn more knowledge, welcome to follow the industry information channel!

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