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8
votes
1
answer
196
views
1
answer
How extract the longest overlap?
bedtools deeptools bedops intersect overlap written 17 days ago by star • 130 • updated 14 days ago by Biostar ♦♦ 20
7
votes
3
answers
2.1k
views
3
answers
Finding Chip Seq Overlaps with Bed files
bedtools chip-seq bedops bedmap written 3.3 years ago by morovatunc • 400
4
votes
1
answer
223
views
1
answer
BEDOPS bedmap tool usage
bedops sequence bedmap dna written 3 months ago by Uday Rangaswamy • 100 • updated 3 months ago by Alex Reynolds ♦ 27k
1
vote
1
answer
197
views
1
answer
BEDOPS installation on MAC
assembly bedops written 3 months ago by MK2000 • 30 • updated 3 months ago by Alex Reynolds ♦ 27k
7
votes
5
answers
217
views
5 follow
5
answers
Pulling out interval adjoining regions
bedtools bed bedops interval written 3 months ago by rbronste • 230 • updated 3 months ago by Alex Reynolds ♦ 27k
0
votes
0
answers
167
views
0
answers
Closest features sort by set distance
bedtools bed bedops intervals written 4 months ago by rbronste • 230
0
votes
1
answer
183
views
1
answer
Read depth interval comparison
read depth bed bedops bam bedtools written 4 months ago by rbronste • 230 • updated 4 months ago by Pierre Lindenbaum ♦ 118k
3
votes
2
answers
200
views
2
answers
Extending BED intervals
bedtools bed bedops interval written 4 months ago by rbronste • 230 • updated 4 months ago by Alex Reynolds ♦ 27k
1
vote
1
answer
171
views
1
answer
BEDOPS sort-bed BED_LINE_LEN question
bed bedops intervals sort-bed written 5 months ago by rbronste • 230
4
votes
2
answers
2.0k
views
2
answers
split bed file into several bed files where each region is separated of any other by N bases
bedtools bed bedops written 3.1 years ago by 14134125465346445 • 3.4k • updated 6 months ago by RamRS ♦ 20k
2
votes
1
answer
325
views
1
answer
Merge intervals between but NOT within 2 BED files
bedtools overlap merge bedops written 6 months ago by Anand Rao • 210 • updated 6 months ago by Alex Reynolds ♦ 27k
7
votes
2
answers
306
views
2
answers
Finding closest downstream gene including overlap 3' ends
bedtools bedops written 9 months ago by jfelds11 • 20
0
votes
0
answers
715
views
0
answers
Average PhastCon score using bedops
software error bedops starch written 2.4 years ago by Shaway • 10 • updated 10 months ago by Biostar ♦♦ 20
7
votes
2
answers
439
views
7 follow
2
answers
How to extract genes 10000 bp upstream and 1000 bp downstream of long non coding RNA?
bedtools bedops awk sed bash written 12 months ago by bk11 • 30 • updated 12 months ago by Alex Reynolds ♦ 27k
1
vote
2
answers
652
views
2
answers
Stats on the overlapping length within two bed files
bedtools genome bedops written 12 months ago by beanavarro85 • 0 • updated 12 months ago by Alex Reynolds ♦ 27k
2
votes
1
answer
313
views
1
answer
Bedops --element-of misses elements
bedops --element-of written 13 months ago by rs • 40 • updated 13 months ago by Alex Reynolds ♦ 27k
0
votes
1
answer
391
views
1
answer
How to rewrite convert2bed function from BEDOps using GNU parallel for batch processing?
bedops parallel convert2bed written 14 months ago by texaswhiskey1969 • 0 • updated 14 months ago by jean.elbers • 740
0
votes
0
answers
385
views
0
answers
How to crop gff feature into pieces when an overlap is found
bedtools annotation gff bedops genome written 14 months ago by rimjhim.roy.ch • 70
3
votes
1
answer
706
views
1
answer
FIMO output to bed
bedtools fimo meme bedops written 14 months ago by rbronste • 230 • updated 14 months ago by YaGalbi • 1.4k
1
vote
1
answer
522
views
1
answer
bedops gff2bed error
bedops gff2bed written 14 months ago by varsha619 • 70 • updated 14 months ago by Alex Reynolds ♦ 27k
4
votes
1
answer
374
views
1
answer
bedops -u does not work properly
bed bedops intersect written 14 months ago by Ming Tang • 2.4k • updated 14 months ago by Alex Reynolds ♦ 27k
0
votes
2
answers
468
views
2
answers
VCF to BED conversion error in BEDOPS
vcf bed bedops written 15 months ago by Shab86 • 240 • updated 15 months ago by Alex Reynolds ♦ 27k
6
votes
1
answer
886
views
1
answer
bedops vcf2bed core dump
bedops vcf2bed written 16 months ago by RamRS ♦ 20k
5
votes
2
answers
603
views
2
answers
Recompile bedops with increased TOKENS_MAX_LENGTH
sort-bed bedops written 16 months ago by RamRS ♦ 20k • updated 16 months ago by Alex Reynolds ♦ 27k
10
votes
3
answers
843
views
5 follow
3
answers
bedops vcf2bed eats up all allocated memory
hpc bedops vcf2bed written 16 months ago by RamRS ♦ 20k
3
votes
4
answers
4.0k
views
4
answers
Intersect multiple bed and keep all fields
bedtools bed bedops written 3.6 years ago by user230613 • 270 • updated 17 months ago by ashmc • 0
0
votes
0
answers
483
views
0
answers
Merging bed intervals within a group
bedtools bed bedops written 19 months ago by EVR • 510
0
votes
0
answers
584
views
0
answers
Creating reproducible peak regions from multiple ChIP-seq studies
bedtools bedops written 21 months ago by James Ashmore • 2.6k • updated 19 months ago by Biostar ♦♦ 20
4
votes
1
answer
801
views
1
answer
Closest gene to set of intervals
bedtools bedops written 21 months ago by rbronste • 230 • updated 21 months ago by Rohit • 1.3k
6
votes
1
answer
1.5k
views
1
answer
Merge bed files, keep the peak count
bedtools bedops chip-seq written 2.8 years ago by rioualen • 330 • updated 21 months ago by Biostar ♦♦ 20
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