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GC & AT content calculation

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 :)

chip-seq next-gen r genome
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updated by simon.vanheeringen simon.vanheeringen • written by anu014 anu014

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

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written by Devon Ryan Devon Ryan

Thanks Devon. I realized it now..

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written by anu014 anu014

1 answer

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
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written by simon.vanheeringen simon.vanheeringen

Thank you Simon. It's perfect!

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written by anu014 anu014

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