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54
votes
10
answers
7.9k
views
9 follow
10
answers
Tool: Bedtools: Analyzing Genomic Features
bedtools tool written 8.3 years ago by Istvan Albert ♦♦ 84k • updated 5.6 years ago by Aaronquinlan ♦ 11k
118
votes
8
answers
56k
views
80 follow
8
answers
Tutorial: Piping With Samtools, Bwa And Bedtools
bedtools tutorial samtools unix bwa written 8.3 years ago by Ying W • 4.0k • updated 4.7 years ago by Yaseen Ladak • 30
10
votes
7
answers
5.0k
views
7 follow
7
answers
randomly shuffle BAM file
bedtools bam shuffle written 5.1 years ago by mparker2 • 20 • updated 3.3 years ago by skanterakis • 110
36
votes
6
answers
11k
views
19 follow
6
answers
Annotating Genomic Intervals
bedtools annotation bioconductor R written 7.9 years ago by Stephen ♦ 2.7k • updated 7.9 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 7.5 years ago by user • 850 • updated 11 months ago by ATpoint ♦ 36k
11
votes
5
answers
18k
views
9 follow
5
answers
How Can I Compare And Merge Bed Files
bedtools bed written 8.1 years ago by lyfsa • 30 • updated 7.3 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 7.4 years ago by Surya Saha • 260 • updated 6.8 years ago by plafdesigns • 40
30
votes
5
answers
25k
views
17 follow
5
answers
Bedtools Genomecoveragebed Usage : How To Create A Genome File?
bedtools written 7.3 years ago by komal.rathi • 3.6k • updated 9 months ago by Phoenix Mu • 20
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 7.2 years ago by Malachi Griffith ♦ 18k • updated 21 months ago by Paul • 1.4k
2
votes
5
answers
862
views
6 follow
5
answers
Expanding Genomic Coordinates Using Bedtools
bedtools bed tools genomc bed file written 2.2 years ago by gtasource • 60 • updated 2.1 years ago by Aaronquinlan ♦ 11k
6
votes
5
answers
857
views
5 follow
5
answers
Extract start coordinate from read 1 and end coordinate from read 2 of paired end reads.
bedtools unix written 23 months ago by rjobmc • 0 • updated 23 months ago by finswimmer ♦ 13k
7
votes
5
answers
423
views
5 follow
5
answers
Pulling out interval adjoining regions
bedtools bed bedops interval written 20 months ago by rbronste • 360 • updated 20 months ago by Alex Reynolds ♦ 30k
32
votes
4
answers
14k
views
17 follow
4
answers
Getting Unmapped Reads: Comparing Fastq To Bam
bedtools fastq bam samtools written 8.7 years ago by User 9996 • 810 • updated 8.7 years ago by brentp ♦ 23k
3
votes
4
answers
9.7k
views
5 follow
4
answers
Genomecoveragebed - Bedtool For Reporting Per Base Genome Coverage
bedtools coverage written 8.5 years ago by Varun Gupta • 1.1k • updated 6.6 years ago by hygine555 • 0
4
votes
4
answers
3.8k
views
6 follow
4
answers
Extract Only Paired-End Reads That Map A Specific Interval
bedtools extraction written 8.0 years ago by Nicolas Rosewick ♦ 9.0k • updated 22 months ago by pnatsidis • 0
5
votes
4
answers
6.2k
views
5 follow
4
answers
N Closest Genes To A Given Location
bedtools intersect written 7.9 years ago by dfernan • 690 • updated 7.9 years ago by Alex Reynolds ♦ 30k
20
votes
4
answers
9.3k
views
10 follow
4
answers
How To Extract Scores From Bedgraph File Using Bed Tools
bedtools written 7.6 years ago by biorepine • 1.5k • updated 17 months ago by brianpenghe • 20
5
votes
4
answers
2.1k
views
5 follow
4
answers
Tool For Binning Windowbed Output For K-Means Clustering
bedtools chip-seq clustering heatmap written 6.9 years ago by bede.portz • 490
1
vote
4
answers
4.8k
views
5 follow
4
answers
To Calculate The Exact Total Number Of Mapped Reads In Exome Regions
bedtools gatk ngs exome-sequencing coverage written 6.7 years ago by ivivek_ngs • 5.0k • updated 6.7 years ago by Wei Shi • 0
14
votes
4
answers
6.4k
views
6 follow
4
answers
Calculating GC content from BAM file by BED file
cg content bed bam bedtools written 5.7 years ago by Paul • 1.4k • updated 5.7 years ago by Aaronquinlan ♦ 11k
4
votes
4
answers
5.3k
views
4
answers
Intersect multiple bed and keep all fields
bedtools bed bedops written 5.0 years ago by user230613 • 280 • updated 2.8 years ago by ashmc • 0
1
vote
4
answers
931
views
4
answers
Generate bed co-ordinates other then given input bed file
bedfile bedtools written 4.2 years ago by Chirag Parsania • 1.8k • updated 4.2 years ago by A. Domingues • 2.3k
0
votes
4
answers
1.6k
views
4
answers
condition bedtools on name column
bedtools written 4.0 years ago by burnsro • 20 • updated 4.0 years ago by Alex Reynolds ♦ 30k
15
votes
4
answers
8.2k
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 3.5 years ago by tara.alpert • 30 • updated 15 months ago by iqra • 0
6
votes
4
answers
2.2k
views
4
answers
bedtools - getfasta: How to report both 'chrom:start-stop and' 'name' of sequence?
bedtools written 2.3 years ago by bi_Scholar • 0 • updated 2.3 years ago by Alex Reynolds ♦ 30k
7
votes
3
answers
8.2k
views
5 follow
3
answers
Convert .Txt Into Bed Files
bedtools comparison written 9.1 years ago by Bioscientist • 1.7k • updated 9.1 years ago by Swbarnes2 • 1.5k
88
votes
3
answers
51k
views
33 follow
3
answers
Bedtools Compare Multiple Bed Files?
bedtools intersect written 8.8 years ago by Bioscientist • 1.7k • updated 7.6 years ago by sjneph • 620
7
votes
3
answers
5.9k
views
5 follow
3
answers
Reporting The Bam Reads Overlapping A Set Of Intervals With Bedtools
bedtools bed next-gen bam sequencing written 8.8 years ago by User 9996 • 810 • updated 8.8 years ago by Alex Reynolds ♦ 30k
13
votes
3
answers
8.9k
views
5 follow
3
answers
Multi Thread Bedtools
bedtools parallel written 8.7 years ago by Nicolas Rosewick ♦ 9.0k • updated 6.1 years ago by Biostar ♦♦ 20
28
votes
3
answers
6.2k
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 8.5 years ago by Sander Timmer • 700 • updated 8.5 years ago by David Langenberger ♦ 9.5k
<prev • 581 results • page 1 of 20 • next >
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