Is there a software for genomic calculation of GC content and Gene density under sliding windows?
Is there a software for genomic calculation of GC content and Gene density under sliding windows?
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weishang •
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weishang •
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What is "genomic statistical calculation of GC content "? So just determining the GC content?
E.g. make the sliding windows with
bedtools makewindows(this gives you a BED file), and then together with a fasta file of the genome use: A: Calculating Gc Content For All CcdsYes I mean GC content, sorry for the mistake, I have just remove that word.
Ok, no problem. Does the suggested solution make sense to you or do you need something else?
Yes, the gene density under sliding windows
I would probably intersect the sliding window BED file with a BED file that contains only the TSS (transcription start site) coordinates of every gene (or rather transcript), e.g. bedtools
intersectand from this make the calculation.