bedops-discuss

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1–15 of 15

Welcome to the BEDOPS discussion group! Here, we field questions and comments about the BEDOPS suite, using bedops, bedmap, bedextract, closest-features, sort-bed, starch and other tools used for high-performance genomics analysis. We hope that you find this resource useful in making the most of this toolkit!

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Thijmen B, Alex Reynolds4

4/15/20

Problem with running gff2bed

Thanks for posting a link to the original file. Here's one way you might debug and fix this issue

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Problem with running gff2bed

Thanks for posting a link to the original file. Here's one way you might debug and fix this issue

4/15/20

JL, … Brad Gulko7

7/30/16

Problem with intersect bed files: missing chr10-22,Y

Just to close the loop on the second issue, I do not reproduce your results. When I create 2 bed

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Problem with intersect bed files: missing chr10-22,Y

Just to close the loop on the second issue, I do not reproduce your results. When I create 2 bed

7/30/16

9/22/15

Re: Digest for bedops-discuss@googlegroups.com - 4 updates in 1 topic

Consider: bedmap --echo-ref-name --echo-map regions.bed main.bed \ | awk -F"|" 'BEGIN {

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Re: Digest for bedops-discuss@googlegroups.com - 4 updates in 1 topic

Consider: bedmap --echo-ref-name --echo-map regions.bed main.bed \ | awk -F"|" 'BEGIN {

9/22/15

francy....@gmail.com, Alex Reynolds4

9/21/15

output overlap for each region in a file

Thank you Alex! But this is not giving me what I was looking for though, it gives me many output

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output overlap for each region in a file

Thank you Alex! But this is not giving me what I was looking for though, it gives me many output

9/21/15

1/9/14

BEDOPS v2.4 released

BEDOPS is a suite of tools to address common questions raised in genomic studies — mostly with regard

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BEDOPS v2.4 released

BEDOPS is a suite of tools to address common questions raised in genomic studies — mostly with regard

1/9/14

12/26/13

Re: Digest for bedops-discuss@googlegroups.com - 1 Message in 1 Topic

It should also be noted that the comparison to bedmap is a special case. In all problems related to

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Re: Digest for bedops-discuss@googlegroups.com - 1 Message in 1 Topic

It should also be noted that the comparison to bedmap is a special case. In all problems related to

12/26/13

12/24/13

Re: Digest for bedops-discuss@googlegroups.com - 3 Messages in 1 Topic

I don't seem to get the updates for this group except these digests for some reason. Any

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Re: Digest for bedops-discuss@googlegroups.com - 3 Messages in 1 Topic

I don't seem to get the updates for this group except these digests for some reason. Any

12/24/13

Gert Hulselmans, Alex Reynolds5

12/23/13

BEDOPS benchmarks

On Dec 23, 2013, at 5:19 PM, Gert Hulselmans <hulselm...@gmail.com> wrote: > It would be

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BEDOPS benchmarks

On Dec 23, 2013, at 5:19 PM, Gert Hulselmans <hulselm...@gmail.com> wrote: > It would be

12/23/13

10/15/13

BEDOPS v2.3 released

We have released BEDOPS v2.3, including bug fixes for starch and starch-dependent tools, improved

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BEDOPS v2.3 released

We have released BEDOPS v2.3, including bug fixes for starch and starch-dependent tools, improved

10/15/13

owwa, Alex Reynolds14

7/7/13

bedops installation error

Hi Alex, thank you so much for your kind help! I have made a smaller BAM file, could you please check

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bedops installation error

Hi Alex, thank you so much for your kind help! I have made a smaller BAM file, could you please check

7/7/13

Margaret H, … Margaret Ho3

7/2/13

ERROR: Total amount of bytes read not equal to Starch v2 metadata length

Hi Alex and Bob, Thank you both for your responses. Switching to the 64-bit version of Bedops solved

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ERROR: Total amount of bytes read not equal to Starch v2 metadata length

Hi Alex and Bob, Thank you both for your responses. Switching to the 64-bit version of Bedops solved

7/2/13

raghav, Alex Reynolds2

6/24/13

EOF marker is absent

Try: $ bam2bed < /storage/home/cdac/raghav/bowtie2-2.1.0/uniquely_SRR681003_1.bam >

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EOF marker is absent

Try: $ bam2bed < /storage/home/cdac/raghav/bowtie2-2.1.0/uniquely_SRR681003_1.bam >

6/24/13

5/26/13

Request for Participation in a Genomic File Format Survey

Hi, I'm a PhD student and could really use some help. I'm trying to finish my dissertation

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Request for Participation in a Genomic File Format Survey

Hi, I'm a PhD student and could really use some help. I'm trying to finish my dissertation

5/26/13

5/23/13

BEDOPS 2.2 released

We have released BEDOPS v2.2, including bug fixes for unstarch and starchcat, and reversion to the C-

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BEDOPS 2.2 released

We have released BEDOPS v2.2, including bug fixes for unstarch and starchcat, and reversion to the C-

5/23/13

5/3/13

BEDOPS v2.1.1 released

We have released BEDOPS v2.1.1, including significant performance enhancements to bedmap and bug

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BEDOPS v2.1.1 released

We have released BEDOPS v2.1.1, including significant performance enhancements to bedmap and bug

5/3/13

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