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118
votes
8
answers
59k
views
80 follow
8
answers
Tutorial: Piping With Samtools, Bwa And Bedtools
bedtools tutorial samtools unix bwa written 8.7 years ago by Ying W4.0k • updated 5.2 years ago by Yaseen Ladak30
90
votes
3
answers
54k
views
35 follow
3
answers
Bedtools Compare Multiple Bed Files?
bedtools intersect written 9.2 years ago by Bioscientist1.7k • updated 8.0 years ago by sjneph620
36
votes
6
answers
12k
views
19 follow
6
answers
Annotating Genomic Intervals
bedtools annotation bioconductor R written 8.3 years ago by Stephen2.7k • updated 8.3 years ago by Alex Reynolds31k
32
votes
6
answers
27k
views
19 follow
6
answers
Converting Bam To Bedgraph For Viewing On Ucsc?
bedtools bed bam genome-browser ucsc written 7.9 years ago by user870 • updated 17 months ago by ATpoint44k
32
votes
4
answers
14k
views
17 follow
4
answers
Getting Unmapped Reads: Comparing Fastq To Bam
bedtools fastq bam samtools written 9.1 years ago by User 9996810 • updated 9.1 years ago by brentp23k
32
votes
5
answers
27k
views
17 follow
5
answers
Bedtools Genomecoveragebed Usage : How To Create A Genome File?
bedtools written 7.7 years ago by komal.rathi3.7k • updated 14 months ago by Phoenix Mu40
23
votes
2
answers
8.2k
views
16 follow
2
answers
18
votes
5
answers
14k
views
14 follow
5
answers
Discrepancy In Samtools Mpileup/Depth And Bedtools Genomecoveragebed Counts
bedtools samtools written 7.8 years ago by Surya Saha260 • updated 7.2 years ago by plafdesigns40
15
votes
4
answers
8.9k
views
14 follow
4
answers
32
votes
3
answers
9.1k
views
13 follow
3
answers
Picking Random Genomic Positions
perl bedtools bash written 8.5 years ago by PoGibas4.8k
18
votes
3
answers
11k
views
13 follow
3
answers
Heatmap Of Read Coverage Around Tsss
bedtools coverage heatmap written 7.4 years ago by A. Domingues2.4k • updated 7.3 years ago by Ying W4.0k
25
votes
2
answers
29k
views
11 follow
2
answers
Converting Gff To Bed With Bedtools?
bedtools bed gff conversion written 8.0 years ago by user870 • updated 8.0 years ago by Alex Reynolds31k
20
votes
4
answers
9.7k
views
10 follow
4
answers
How To Extract Scores From Bedgraph File Using Bed Tools
bedtools written 8.0 years ago by biorepine1.5k • updated 22 months ago by brianpenghe50
17
votes
5
answers
8.5k
views
10 follow
5
answers
54
votes
10
answers
8.0k
views
9 follow
10
answers
Tool: Bedtools: Analyzing Genomic Features
bedtools tool written 8.7 years ago by Istvan Albert ♦♦ 86k • updated 6.0 years ago by Aaronquinlan11k
11
votes
5
answers
19k
views
9 follow
5
answers
How Can I Compare And Merge Bed Files
bedtools bed written 8.5 years ago by lyfsa30 • updated 7.7 years ago by beary.pooh10
14
votes
2
answers
4.0k
views
9 follow
2
answers
Converting large (compressed and unsorted) BAM files to fastq
bedtools picard fatsq alignment bam written 4.2 years ago by alesssia570 • updated 4.2 years ago by Brian Bushnell17k
9
votes
2
answers
1.6k
views
9 follow
2
answers
17
votes
3
answers
2.6k
views
8 follow
3
answers
Simple Redirection, I/O Problem With Bedtools
bedtools bash intersect pipeline linux written 8.0 years ago by Sukhi Singh10k • updated 8.0 years ago by Ryan Dale4.9k
8
votes
2
answers
7.7k
views
8 follow
2
answers
Error In Bedtools Getfasta: Chromosome Not Found
bedtools error written 8.0 years ago by Pat Baldrich10 • updated 4.3 years ago by Prakki Rama2.4k
6
votes
3
answers
8.3k
views
8 follow
3
answers
How To Install Bedtools In A User Directory
bedtools written 7.6 years ago by alittleboy220 • updated 6.8 years ago by paulr80
9
votes
2
answers
7.3k
views
8 follow
2
answers
14
votes
1
answer
2.1k
views
8 follow
1
answer
Tutorial: Introduction to bedtools.
bedtools tutorial written 6.2 years ago by Aaronquinlan11k • updated 4.1 years ago by mcc80
28
votes
3
answers
6.4k
views
7 follow
3
answers
20
votes
3
answers
3.8k
views
7 follow
3
answers
How To Find The Nearest Gene To A Retrotransposon Insert?
bedtools bed position mouse written 8.8 years ago by Joseph Hughes2.9k • updated 8.8 years ago by Alex Reynolds31k
10
votes
3
answers
3.7k
views
7 follow
3
answers
How Can I Include One Bed File In Another Bed File ?
bedtools merge written 7.5 years ago by fmfshog0 • updated 7.5 years ago by sjneph620
10
votes
7
answers
5.4k
views
7 follow
7
answers
randomly shuffle BAM file
bedtools bam shuffle written 5.5 years ago by mparker220 • updated 3.7 years ago by skanterakis110
5
votes
1
answer
2.5k
views
7 follow
1
answer
Tutorial: bam2rpkm by bedtools
bedtools rpkm tutorial bam rna-seq written 3.2 years ago by jmzeng1314110 • updated 7 weeks ago by ATpoint44k
7
votes
2
answers
930
views
7 follow
2
answers
3
votes
1
answer
1.3k
views
7 follow
1
answer
Bedtools intersect alternatives available
bedtools written 2.3 years ago by Jeffin Rockey1.2k • updated 2.3 years ago by Alex Reynolds31k
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