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54
votes
10
answers
7.9k
views
9 follow
10
answers
Tool: Bedtools: Analyzing Genomic Features
bedtools tool written 8.5 years ago by Istvan Albert ♦♦ 85k • updated 5.8 years ago by Aaronquinlan ♦ 11k
118
votes
8
answers
57k
views
80 follow
8
answers
Tutorial: Piping With Samtools, Bwa And Bedtools
bedtools tutorial samtools unix bwa written 8.5 years ago by Ying W • 4.0k • updated 5.0 years ago by Yaseen Ladak • 30
10
votes
7
answers
5.2k
views
7 follow
7
answers
randomly shuffle BAM file
bedtools bam shuffle written 5.3 years ago by mparker2 • 20 • updated 3.5 years ago by skanterakis • 110
36
votes
6
answers
11k
views
19 follow
6
answers
Annotating Genomic Intervals
bedtools annotation bioconductor R written 8.1 years ago by Stephen ♦ 2.7k • updated 8.1 years ago by Alex Reynolds ♦ 31k
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 7.7 years ago by user • 850 • updated 14 months ago by ATpoint ♦ 40k
11
votes
5
answers
19k
views
9 follow
5
answers
How Can I Compare And Merge Bed Files
bedtools bed written 8.3 years ago by lyfsa • 30 • updated 7.5 years ago by beary.pooh • 10
18
votes
5
answers
14k
views
14 follow
5
answers
Discrepancy In Samtools Mpileup/Depth And Bedtools Genomecoveragebed Counts
bedtools samtools written 7.6 years ago by Surya Saha • 260 • updated 7.0 years ago by plafdesigns • 40
31
votes
5
answers
26k
views
17 follow
5
answers
Bedtools Genomecoveragebed Usage : How To Create A Genome File?
bedtools written 7.5 years ago by komal.rathi • 3.7k • updated 12 months ago by Phoenix Mu • 40
17
votes
5
answers
8.3k
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 7.5 years ago by Malachi Griffith ♦ 18k • updated 2.0 years ago by Paul • 1.4k
2
votes
5
answers
941
views
6 follow
5
answers
Expanding Genomic Coordinates Using Bedtools
bedtools bed tools genomc bed file written 2.4 years ago by gtasource • 60 • updated 2.3 years ago by Aaronquinlan ♦ 11k
6
votes
5
answers
906
views
5 follow
5
answers
Extract start coordinate from read 1 and end coordinate from read 2 of paired end reads.
bedtools unix written 2.2 years ago by rjobmc • 0 • updated 2.2 years ago by finswimmer ♦ 14k
7
votes
5
answers
449
views
5 follow
5
answers
Pulling out interval adjoining regions
bedtools bed bedops interval written 23 months ago by rbronste • 360 • updated 23 months ago by Alex Reynolds ♦ 31k
32
votes
4
answers
14k
views
17 follow
4
answers
Getting Unmapped Reads: Comparing Fastq To Bam
bedtools fastq bam samtools written 8.9 years ago by User 9996 • 810 • updated 8.9 years ago by brentp ♦ 23k
3
votes
4
answers
9.8k
views
5 follow
4
answers
Genomecoveragebed - Bedtool For Reporting Per Base Genome Coverage
bedtools coverage written 8.7 years ago by Varun Gupta • 1.2k • updated 6.8 years ago by hygine555 • 0
4
votes
4
answers
3.9k
views
6 follow
4
answers
Extract Only Paired-End Reads That Map A Specific Interval
bedtools extraction written 8.2 years ago by Nicolas Rosewick ♦ 9.2k • updated 2.1 years ago by pnatsidis • 0
5
votes
4
answers
6.3k
views
5 follow
4
answers
N Closest Genes To A Given Location
bedtools intersect written 8.1 years ago by dfernan • 690 • updated 8.1 years ago by Alex Reynolds ♦ 31k
20
votes
4
answers
9.5k
views
10 follow
4
answers
How To Extract Scores From Bedgraph File Using Bed Tools
bedtools written 7.8 years ago by biorepine • 1.5k • updated 20 months ago by brianpenghe • 30
5
votes
4
answers
2.2k
views
5 follow
4
answers
Tool For Binning Windowbed Output For K-Means Clustering
bedtools chip-seq clustering heatmap written 7.1 years ago by bede.portz • 490
1
vote
4
answers
4.9k
views
5 follow
4
answers
To Calculate The Exact Total Number Of Mapped Reads In Exome Regions
bedtools gatk ngs exome-sequencing coverage written 6.9 years ago by ivivek_ngs • 5.0k • updated 6.9 years ago by Wei Shi • 0
14
votes
4
answers
6.7k
views
6 follow
4
answers
Calculating GC content from BAM file by BED file
cg content bed bam bedtools written 5.9 years ago by Paul • 1.4k • updated 5.9 years ago by Aaronquinlan ♦ 11k
4
votes
4
answers
5.5k
views
4
answers
Intersect multiple bed and keep all fields
bedtools bed bedops written 5.2 years ago by user230613 • 280 • updated 3.0 years ago by Ashley M. Conard • 0
1
vote
4
answers
949
views
4
answers
Generate bed co-ordinates other then given input bed file
bedfile bedtools written 4.5 years ago by Chirag Parsania • 1.9k • updated 4.4 years ago by A. Domingues • 2.3k
0
votes
4
answers
1.7k
views
4
answers
condition bedtools on name column
bedtools written 4.2 years ago by burnsro • 20 • updated 4.2 years ago by Alex Reynolds ♦ 31k
15
votes
4
answers
8.5k
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 3.7 years ago by tara.alpert • 30 • updated 17 months ago by iqra • 0
6
votes
4
answers
2.4k
views
4
answers
bedtools - getfasta: How to report both 'chrom:start-stop and' 'name' of sequence?
bedtools written 2.5 years ago by bi_Scholar • 0 • updated 2.5 years ago by Alex Reynolds ♦ 31k
7
votes
3
answers
8.4k
views
5 follow
3
answers
Convert .Txt Into Bed Files
bedtools comparison written 9.3 years ago by Bioscientist • 1.7k • updated 9.3 years ago by Swbarnes2 • 1.5k
89
votes
3
answers
53k
views
33 follow
3
answers
Bedtools Compare Multiple Bed Files?
bedtools intersect written 9.0 years ago by Bioscientist • 1.7k • updated 7.8 years ago by sjneph • 620
7
votes
3
answers
6.0k
views
5 follow
3
answers
Reporting The Bam Reads Overlapping A Set Of Intervals With Bedtools
bedtools bed next-gen bam sequencing written 9.0 years ago by User 9996 • 810 • updated 9.0 years ago by Alex Reynolds ♦ 31k
13
votes
3
answers
9.2k
views
5 follow
3
answers
Multi Thread Bedtools
bedtools parallel written 8.9 years ago by Nicolas Rosewick ♦ 9.2k • updated 6.3 years ago by Biostar ♦♦ 20
28
votes
3
answers
6.3k
views
7 follow
3
answers
Converting Sam Files To Bam Files - Reproduce Results Nature Paper: Transcriptome Genetics Using Second Generation Sequencing In A Caucasian Population
bedtools bam samtools sam written 8.7 years ago by Sander Timmer • 700 • updated 8.7 years ago by David Langenberger ♦ 9.5k
<prev • 598 results • page 1 of 20 • next >
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