GC content graph

Question

[sayna_shahdparvar]

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.

[GenoMax]

For a whole genome ? isochore from EMBOSS.

Answer 1

[Prasad]

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

[GenoMax]

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

[Prasad]

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

Answer 2

[dariober]

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.