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Forum: Bioinformatics 08-25-2015, 09:03 AM
Replies: 0
Views: 1,002
Posted By ninja_help
bedtools

Hi all

I am currently working with bedtools and need a suggestion.
I am using the -name option to have it give me the names the that the sequence correlates to.

But I noticed that the -tab...
Forum: Bioinformatics 08-13-2015, 08:08 AM
Replies: 2
Views: 1,154
Posted By ninja_help
ahh I tried that on a much shorted example but...

ahh I tried that on a much shorted example but didnt flip the coordinates. Thanks!
Forum: Bioinformatics 08-13-2015, 07:53 AM
Replies: 2
Views: 1,154
Posted By ninja_help
bedtools giving me an error, new program suggestions?

Hi all

Recently I started using bedtools as a way of analyzing a genome, it was working fantastically. But I ran into an error which is making me look into other methods of analyzing a genome...
Forum: Bioinformatics 08-07-2015, 10:43 AM
Replies: 4
Views: 930
Posted By ninja_help
I have another question regarding the BED format...

I have another question regarding the BED format (my apologies for so many questions)
I dont know what scaffold the locations are located on, would that impair me from using BED
since they require...
Forum: Bioinformatics 08-07-2015, 08:45 AM
Replies: 4
Views: 930
Posted By ninja_help
thanks for the reply @dgscofield by BED3...

thanks for the reply @dgscofield

by BED3 format do you mean this (https://genome.ucsc.edu/FAQ/FAQformat.html#format1) under the BED format section?
Forum: Bioinformatics 08-06-2015, 02:12 PM
Replies: 4
Views: 930
Posted By ninja_help
using bioperl to parse genome based on basepair location

Hello all
I have a genome that I am looking to parse a genome based on another file that has a name associated with the coordinates of the specific name in the genome of my species (for this purpose...
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