GC & AT content calculation

Question

[anu014]

Hello Biostars,

Can anyone tell me how can I get GC & AT percentage in chip-seq peak bed file?
I have seen that GC content can be calculated using UCSC browser & EMBOSS suit itself. But I am not getting any tool for AT calculation.

Please suggest me some methods. Thank you :)

[Devon Ryan]

If you're able to get GC content, then AT content is just 1 minus that.

[anu014]

Thanks Devon. I realized it now..

Answer 1

[simon.vanheeringen]

You can use bedtools.

bedtools nuc -fi /data/genomes/hg38/hg38.fa -bed input.bed | cut -f1-5

#1_usercol  2_usercol   3_usercol   4_pct_at    5_pct_gc
chr1    28216   31238   0.465255    0.534745
chr1    51379   52104   0.478621    0.521379
chr1    136251  145899  0.473984    0.526016

[anu014]

Thank you Simon. It's perfect!