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Old 08-13-2014, 03:59 PM   #1
rashmijain
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Default percentage of repeat region every 500kb

I have gff3 file for repeat region, which shows repeat start and end position. I want to calculate what is % of repeat region in every 500 kb.
I have tried to find it on internet, but didn't find.

Any help is appreciated!

Thank you

Rashmi
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Old 08-14-2014, 08:13 AM   #2
westerman
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I suspect that you will have to write some code to parse out the GFF and output what you want. This does not seem like a common request and thus I doubt if there is pre-existing code.
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Old 08-14-2014, 08:18 AM   #3
rashmijain
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Thank you for the reply.....
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Old 08-18-2014, 04:18 AM   #4
syfo
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I'd try with bedtools. Something like converting the gff to bed, generate a bed file with 500Kb genomic bins, run bedtools intersect or coverage to get the overlap in each bin and parse the resulting output to compute the precise values. If you have some knowledge on bioinformatics that should not be too problematic.
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Old 08-18-2014, 10:18 AM   #5
rashmijain
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Hi Thank you for the reply

we have written code for that.
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