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118
votes
8
answers
57k
views
80 follow
8
answers
Tutorial: Piping With Samtools, Bwa And Bedtools
bedtools tutorial samtools unix bwa written 8.4 years ago by Ying W • 4.0k • updated 4.9 years ago by Yaseen Ladak • 30
88
votes
3
answers
52k
views
33 follow
3
answers
Bedtools Compare Multiple Bed Files?
bedtools intersect written 8.9 years ago by Bioscientist • 1.7k • updated 7.7 years ago by sjneph • 620
25
votes
2
answers
27k
views
11 follow
2
answers
Converting Gff To Bed With Bedtools?
bedtools bed gff conversion written 7.7 years ago by user • 850 • updated 7.7 years ago by Alex Reynolds ♦ 30k
32
votes
6
answers
26k
views
19 follow
6
answers
Converting Bam To Bedgraph For Viewing On Ucsc?
bedtools bed bam genome-browser ucsc written 7.6 years ago by user • 850 • updated 12 months ago by ATpoint ♦ 38k
30
votes
5
answers
26k
views
17 follow
5
answers
Bedtools Genomecoveragebed Usage : How To Create A Genome File?
bedtools written 7.4 years ago by komal.rathi • 3.7k • updated 10 months ago by Phoenix Mu • 40
25
votes
1
answer
23k
views
6 follow
1
answer
How To Use Bedtools To Extract Promoters From A Mouse Bed File
bedtools bed extraction promoter fasta written 8.6 years ago by Anima Mundi • 2.7k • updated 8.6 years ago by Aaronquinlan ♦ 11k
11
votes
5
answers
18k
views
9 follow
5
answers
How Can I Compare And Merge Bed Files
bedtools bed written 8.2 years ago by lyfsa • 30 • updated 7.4 years ago by beary.pooh • 10
32
votes
4
answers
14k
views
17 follow
4
answers
Getting Unmapped Reads: Comparing Fastq To Bam
bedtools fastq bam samtools written 8.8 years ago by User 9996 • 810 • updated 8.8 years ago by brentp ♦ 23k
18
votes
5
answers
14k
views
14 follow
5
answers
Discrepancy In Samtools Mpileup/Depth And Bedtools Genomecoveragebed Counts
bedtools samtools written 7.5 years ago by Surya Saha • 260 • updated 6.9 years ago by plafdesigns • 40
14
votes
3
answers
12k
views
3
answers
Error: unable to open file or unable to determine types for file bed file
bedtools bed sequencing written 5.7 years ago by sebastianzeki0 • 180
36
votes
6
answers
11k
views
19 follow
6
answers
Annotating Genomic Intervals
bedtools annotation bioconductor R written 8.0 years ago by Stephen ♦ 2.7k • updated 8.0 years ago by Alex Reynolds ♦ 30k
18
votes
3
answers
10k
views
13 follow
3
answers
Heatmap Of Read Coverage Around Tsss
bedtools coverage heatmap written 7.1 years ago by A. Domingues • 2.3k • updated 7.0 years ago by Ying W • 4.0k
3
votes
4
answers
9.7k
views
5 follow
4
answers
Genomecoveragebed - Bedtool For Reporting Per Base Genome Coverage
bedtools coverage written 8.6 years ago by Varun Gupta • 1.1k • updated 6.7 years ago by hygine555 • 0
2
votes
1
answer
9.4k
views
1
answer
Coveragebed, Depth/Breadth Of Coverage
bedtools coverage written 9.3 years ago by Newbionf • 10 • updated 9.3 years ago by Istvan Albert ♦♦ 84k
20
votes
4
answers
9.4k
views
10 follow
4
answers
How To Extract Scores From Bedgraph File Using Bed Tools
bedtools written 7.7 years ago by biorepine • 1.5k • updated 18 months ago by brianpenghe • 30
12
votes
3
answers
9.2k
views
3
answers
How to generate BedGraph from BedTools Coverage?
bedtools bed genomic written 5.0 years ago by SmallChess • 530 • updated 5.0 years ago by Alex Reynolds ♦ 30k
13
votes
3
answers
9.0k
views
5 follow
3
answers
Multi Thread Bedtools
bedtools parallel written 8.8 years ago by Nicolas Rosewick ♦ 9.0k • updated 6.2 years ago by Biostar ♦♦ 20
1
vote
1
answer
8.9k
views
1
answer
bedtools merge, ERROR: file has non positional records, which are only valid for the groupBy tool.
bedtools written 3.8 years ago by bio315eskildsen • 10
9
votes
2
answers
8.8k
views
2
answers
Can't convert paired end BAM to bed using bedtools
bedtools alignment bam written 5.2 years ago by colin.kern • 920 • updated 5.1 years ago by guillermofernandeznegrete • 0
32
votes
3
answers
8.8k
views
13 follow
3
answers
Picking Random Genomic Positions
perl bedtools bash written 8.2 years ago by PoGibas ♦ 4.8k
10
votes
2
answers
8.4k
views
5 follow
2
answers
How To Get Annotation For Bed File From Another Bed File
bedtools annotation written 7.8 years ago by k.nirmalraman • 1.0k • updated 5.8 years ago by Biostar ♦♦ 20
15
votes
2
answers
8.4k
views
2
answers
Reproduce Encode/Cshl Long Rna-Seq Data Visualization Viewed In Ucsc, But Failed? [Done]
bedtools encode visualization rna-seq written 8.0 years ago by Puriney • 330 • updated 8.0 years ago by Malachi Griffith ♦ 18k
15
votes
4
answers
8.3k
views
14 follow
4
answers
bedtools coverage gives error received illegal bin number, but that number isn't in my data!
bedtools bin chip-seq coverage error written 3.6 years ago by tara.alpert • 30 • updated 16 months ago by iqra • 0
7
votes
3
answers
8.3k
views
5 follow
3
answers
Convert .Txt Into Bed Files
bedtools comparison written 9.2 years ago by Bioscientist • 1.7k • updated 9.2 years ago by Swbarnes2 • 1.5k
17
votes
5
answers
8.2k
views
10 follow
5
answers
What Is The Fastest Method To Determine The Number Of Positions In A Bam File With >N Coverage?
bedtools depth-of-coverage bam samtools coverage written 7.3 years ago by Malachi Griffith ♦ 18k • updated 23 months ago by Paul • 1.4k
6
votes
3
answers
8.0k
views
8 follow
3
answers
How To Install Bedtools In A User Directory
bedtools written 7.2 years ago by alittleboy • 220 • updated 6.5 years ago by paulr • 80
2
votes
2
answers
8.0k
views
2
answers
Samtools or Bedtools: How to filter a bam file with a bed file using strand information
bedtools bed bam samtools sam written 6.3 years ago by retrogenomics • 20 • updated 6.3 years ago by Alex Reynolds ♦ 30k
5
votes
1
answer
8.0k
views
1
answer
Intersectbed - Overlap Analysis Usign Vcf And Bed Files
bedtools written 8.2 years ago by Khader Shameer ♦ 18k • updated 8.2 years ago by Sukhdeep Singh ♦ 10k
23
votes
2
answers
7.9k
views
16 follow
2
answers
How To Count Genes In Genomic Regions Using A Gtf/Gff3 And A Bed File Of Regions
bedtools gtf gff written 7.6 years ago by Nick Crawford • 210
54
votes
10
answers
7.9k
views
9 follow
10
answers
Tool: Bedtools: Analyzing Genomic Features
bedtools tool written 8.4 years ago by Istvan Albert ♦♦ 84k • updated 5.7 years ago by Aaronquinlan ♦ 11k
<prev • 590 results • page 1 of 20 • next >
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