Question: GC & AT content calculation
0
gravatar for anu014
2.9 years ago by
anu014180
India
anu014180 wrote:

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 • 1.8k views
ADD COMMENTlink modified 2.9 years ago by simon.vanheeringen200 • written 2.9 years ago by anu014180
1

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

ADD REPLYlink written 2.9 years ago by Devon Ryan96k

Thanks Devon. I realized it now..

ADD REPLYlink written 2.9 years ago by anu014180
2
gravatar for simon.vanheeringen
2.9 years ago by
simon.vanheeringen200 wrote:

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
ADD COMMENTlink written 2.9 years ago by simon.vanheeringen200

Thank you Simon. It's perfect!

ADD REPLYlink written 2.9 years ago by anu014180
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