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bedtools-discuss

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6/12/23

Using bedtools, How to calculate gene wise coverage?

Warm greetings Sir Aaron My name is Smriti Arora and I am a Data Analyst cum Immunology researcher at

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Using bedtools, How to calculate gene wise coverage?

Warm greetings Sir Aaron My name is Smriti Arora and I am a Data Analyst cum Immunology researcher at

6/12/23

3/3/23

not giving unique values when doing intersectBed between VCF file and BED file

hey I am facing this issue any idea why?So my vcf contains these : chr1 201784568 . TA . . DP=12;MQ=

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not giving unique values when doing intersectBed between VCF file and BED file

hey I am facing this issue any idea why?So my vcf contains these : chr1 201784568 . TA . . DP=12;MQ=

3/3/23

Fabian Blombach

3/3/23

reldist -detail option

Hi, I used bedtools realist with the -detail option to test the result against a uniform distribution

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reldist -detail option

Hi, I used bedtools realist with the -detail option to test the result against a uniform distribution

3/3/23

Liana Engie, … Milind Chauhan4

1/31/23

Bamtobed file not passing is.region.valid (and then segfaults on merge or intersect)

Hi, I am facing the same problem using bedtools. Did you find the solution to this? On Monday, April

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Bamtobed file not passing is.region.valid (and then segfaults on merge or intersect)

Hi, I am facing the same problem using bedtools. Did you find the solution to this? On Monday, April

1/31/23

Melina Klostermann

1/31/23

bedtools merge only overlapping but not book-ended features

Hello, I am buildng a pipeline for iCLIP analyses, that should output single-nuclotide resolution,

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bedtools merge only overlapping but not book-ended features

Hello, I am buildng a pipeline for iCLIP analyses, that should output single-nuclotide resolution,

1/31/23

12/12/22

Missing bed_to_juncs function

Hello I am running a RNA-seq pipeline, and I am at a stage to filter SNPs. I have a junctions.bed

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Missing bed_to_juncs function

Hello I am running a RNA-seq pipeline, and I am at a stage to filter SNPs. I have a junctions.bed

12/12/22

11/21/22

std::invalid_argument

Hello, I am trying to help a researcher using bedtools. Here is the description: I tried to run a

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std::invalid_argument

Hello, I am trying to help a researcher using bedtools. Here is the description: I tried to run a

11/21/22

Greta Bramerdorfer

11/21/22

copyright request

Hi, I have a rather unconventional request to the authors of the web page of bedtools. I want to use

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copyright request

Hi, I have a rather unconventional request to the authors of the web page of bedtools. I want to use

11/21/22

Laurent MANCHON

10/4/22

how to merge adjacent region with same coverage

--Hi all, this is an extract of my big file: chr2 1 501 0 chr2 501 1001 0 chr2 1001 1501 0 chr2 1501

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how to merge adjacent region with same coverage

--Hi all, this is an extract of my big file: chr2 1 501 0 chr2 501 1001 0 chr2 1001 1501 0 chr2 1501

10/4/22

9/12/22

Installation issue

I have tried all of the suggested options for installing bedtools on Ubuntu wsl (windows 10). It

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Installation issue

I have tried all of the suggested options for installing bedtools on Ubuntu wsl (windows 10). It

9/12/22

Y Z, Aaron Quinlan2

8/3/22

error in bedtools merge

In BED format, start is zero-based, so a single nucleotide would have start 1 less than end.

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error in bedtools merge

In BED format, start is zero-based, so a single nucleotide would have start 1 less than end.

8/3/22

Aaron Quinlan, … Shaun Clare6

8/3/22

Re: [bedtools-discuss] How to resolve error: WARNING. chromosome (Fvb0) was not found in the FASTA file. Skipping.

Would it be possible to get the fix for this since I am having the exact same issue. All chromosomes

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Re: [bedtools-discuss] How to resolve error: WARNING. chromosome (Fvb0) was not found in the FASTA file. Skipping.

Would it be possible to get the fix for this since I am having the exact same issue. All chromosomes

8/3/22

1/13/22

Hi all, Happy New Year! We have developed a new, web-based tool for QC and profiling of BED files

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Hi all, Happy New Year! We have developed a new, web-based tool for QC and profiling of BED files

1/13/22

Daiane Hemerich, Aaron Quinlan2

12/12/21

Enhancers overlapping in at least 2/3 of datasets

I would recommend using the multiinter tool to find regions that are shared by at least M (in your

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Enhancers overlapping in at least 2/3 of datasets

I would recommend using the multiinter tool to find regions that are shared by at least M (in your

12/12/21

11/30/21

Re: [bedtools-discuss] Digest for bedtools-discuss@googlegroups.com - 2 updates in 2 topics

Zhiyuan Liu The chromosome is missing, please check it in your Fasta File. On Tue, Nov 30, 2021 at 5:

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Re: [bedtools-discuss] Digest for bedtools-discuss@googlegroups.com - 2 updates in 2 topics

Zhiyuan Liu The chromosome is missing, please check it in your Fasta File. On Tue, Nov 30, 2021 at 5:

11/30/21

Ram Krishan, Aaron Quinlan3

11/29/21

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

Dear Aaron, Thank you very much. It works well for me. Ramky On Sun, Nov 28, 2021 at 5:45 AM <

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

Dear Aaron, Thank you very much. It works well for me. Ramky On Sun, Nov 28, 2021 at 5:45 AM <

11/29/21

11/13/21

bedtools intersect bug

There is a bug in bedtools 2.30 if there is a very long line in both input files, then bedtools

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bedtools intersect bug

There is a bug in bedtools 2.30 if there is a very long line in both input files, then bedtools

11/13/21

Jichen Wen, Aaron Quinlan3

11/4/21

How to delete a genome index

It works! Thanks for your help!🥳 Aaron Quinlan <aaronq...@gmail.com>于2021年10月22日周五06:35写道：

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How to delete a genome index

It works! Thanks for your help!🥳 Aaron Quinlan <aaronq...@gmail.com>于2021年10月22日周五06:35写道：

11/4/21

11/4/21

Dear All, I have a dataset in excel, from which I have to find out mRNA, lncRNA, etc, I do not know

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Dear All, I have a dataset in excel, from which I have to find out mRNA, lncRNA, etc, I do not know

11/4/21

Miikka Voutilainen, Aaron Quinlan2

9/27/21

Potential bug with bedtools intersect

Hi Mikka, Could please show an example of the SAM records with MAPQ>30 and the resulting output

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Potential bug with bedtools intersect

Hi Mikka, Could please show an example of the SAM records with MAPQ>30 and the resulting output

9/27/21

fateme qasem nejad

8/5/21

hi i tried using bedtools fastafromBed to make transcripts from gtf file and when i give the fasta

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hi i tried using bedtools fastafromBed to make transcripts from gtf file and when i give the fasta

8/5/21

8/5/21

'Chromosome was not found in the FASTA file' error

Hey all, I am trying to use getfasta (bedtools v2.30.0) to extract sequences from my reference using

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'Chromosome was not found in the FASTA file' error

Hey all, I am trying to use getfasta (bedtools v2.30.0) to extract sequences from my reference using

8/5/21

Tobias Baril, Aaron Quinlan2

8/3/21

Bedtools Window size variation

Hi Toby, Unfortunately, I can't think of a simple approach to doing this with bedtools on the

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Bedtools Window size variation

Hi Toby, Unfortunately, I can't think of a simple approach to doing this with bedtools on the

8/3/21

Chentao Yang, Aaron Quinlan2

7/1/21

Two adjacent sites were not annotated by gene features using bedtools intersect.

Hi Chentao, These adjacent intervals do not overlap in the zero-based, half-open coordinate system

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Two adjacent sites were not annotated by gene features using bedtools intersect.

Hi Chentao, These adjacent intervals do not overlap in the zero-based, half-open coordinate system

7/1/21

N Cerda, Aaron Quinlan2

6/15/21

Error with the bedtools merge function

Dear Navei, I am unable to reproduce this problem with version 2.30.0. I receive the expected output.

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Error with the bedtools merge function

Dear Navei, I am unable to reproduce this problem with version 2.30.0. I receive the expected output.

6/15/21

Heiner Kuhl, Aaron Quinlan2

3/22/21

Bedtools scf/chr size limitations

Dear Heiner, The latest version (2.30.0) of bedtools should be compatible with chromosomes this large

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Bedtools scf/chr size limitations

Dear Heiner, The latest version (2.30.0) of bedtools should be compatible with chromosomes this large

3/22/21

Tasha, John Urban2

3/22/21

Tool to split DNA positions

Have you tried "bedtools makewindows"? On Mon, Mar 22, 2021 at 9:26 AM Tasha <tassiazoo@

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Tool to split DNA positions

Have you tried "bedtools makewindows"? On Mon, Mar 22, 2021 at 9:26 AM Tasha <tassiazoo@

3/22/21

Bogdan Tanasa, Aaron Quinlan3

3/15/21

annotations of the BEDPE files

Thank you for your message and confirmation, Aaron. all the best wishes, -- bogdan On Monday, March

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annotations of the BEDPE files

Thank you for your message and confirmation, Aaron. all the best wishes, -- bogdan On Monday, March

3/15/21

Bogdan Tanasa, … Aaron Quinlan5

12/8/20

about statistical significance of the overlap

This is an interesting idea. Let me have a look at the complexity and potential speed increases this

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about statistical significance of the overlap

This is an interesting idea. Let me have a look at the complexity and potential speed increases this

12/8/20

Gloria Sheynkman, Aaron Quinlan3

11/25/20

Report name of overlapping features using `bedtools intersect`

Thank you for the answer - bedtools is a dream. On Wednesday, November 25, 2020 at 9:45:06 AM UTC-5

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Report name of overlapping features using `bedtools intersect`

Thank you for the answer - bedtools is a dream. On Wednesday, November 25, 2020 at 9:45:06 AM UTC-5

11/25/20

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