Re: [bedtools-discuss] Digest for bedtools-discuss@googlegroups.com - 1 update in 1 topic

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Ram Krishan

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Nov 16, 2021, 8:56:26 AM11/16/21
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Dear All,  

Greetings!

I want to find out if mRNA overlaps with transposable elements,  also, either mRNA located upstream or downstream of  transposable elements   
I used bedtools, in which I used intersect, function,  I found only overlap mRNA,  now I want to find out mRNA located upstream or downstream of  transposable elements ,

I kindly request you, please give me some suggestions. 

with regards

Ramky


On Sun, Nov 14, 2021 at 5:45 AM <bedtools...@googlegroups.com> wrote:
Jb DIDI <jun...@gmail.com>: Nov 11 02:51PM -0800

There is a bug in bedtools 2.30
 
if there is a very long line in both input files, then bedtools inersect
-wa -wb will not export the full line but only partial . However, there is
not such maximum line length in each row when using bedtools 2.27 intersect
,
 
Hope this bug will be fixed soon!
 
junbai
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Aaron Quinlan

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Nov 27, 2021, 5:27:30 AM11/27/21
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Hi Ramky,

You can use the “window” tool to look for overlaps within a specified number of basepairs from the main interval.  Also, the “closest” tool will report both overlapping intervals, and when there are none, the closest interval or the closest k intervals.

Aaron

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Ram Krishan

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Nov 29, 2021, 10:18:02 AM11/29/21
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Dear Aaron, 

Thank you very much. It works well for me.

Ramky

On Sun, Nov 28, 2021 at 5:45 AM <bedtools...@googlegroups.com> wrote:

Hi Ramky,
 
You can use the “window” tool to look for overlaps within a specified number of basepairs from the main interval. Also, the “closest” tool will report both overlapping intervals, and when there are none, the closest interval or the closest k intervals.
 
Aaron
 
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