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GC content graph

hello everybody,Im new here , I have aproblem with drawing GC content graph vs genome length,I will be so thankful if introduce me a tool or software which can draw this graph for me. thank you.

gene sequencing genome
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updated by dariober dariober • written by sayna_shahdparvar • sayna_shahdparvar

2 answers

For bacterial genomes or single scaffold genomes you can use BRIG. Same thing can be used to visualize multiple genomes.

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written by Prasad Prasad

Is BRIG capable of plotting GC content? The images are hard to see and the description does not say anything about GC.

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written by GenoMax GenoMax

Yes it has an option of ploting both gc content and gc skew

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written by Prasad Prasad

isochore suggested by genomax2 seems to do what you want. Alternatively, a bit lower level, you can use bedtools like:

bedtools makewindows -g hg19.genome -w 1000 \
| nucBed -fi hg19.genome.fasta -bed

Where hg19.genome is a tab separated file of chromosome names and sizes and hg19.genome.fasta the fasta file of interest.

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written by dariober dariober

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