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2
votes
1
answer
9.4k
views
1
answer
Coveragebed, Depth/Breadth Of Coverage
bedtools coverage written 9.1 years ago by Newbionf • 10 • updated 9.1 years ago by Istvan Albert ♦♦ 84k
7
votes
3
answers
8.1k
views
5 follow
3
answers
Convert .Txt Into Bed Files
bedtools comparison written 9.1 years ago by Bioscientist • 1.7k • updated 9.0 years ago by Swbarnes2 • 1.5k
3
votes
1
answer
6.9k
views
1
answer
Bed File Bedpe Format
bedtools bed bam conversion written 9.0 years ago by Assa Yeroslaviz • 1.4k • updated 2.3 years ago by Biostar ♦♦ 20
7
votes
1
answer
5.5k
views
1
answer
Fastafrombed Problem
bedtools bed conversion fasta written 8.9 years ago by Sara • 130 • updated 8.9 years ago by Pierre Lindenbaum ♦ 129k
5
votes
0
answers
3.6k
views
0
answers
Counting Number Of Bam Reads Directly Within Set Of Intervals With Bedtools
bedtools bed gff bam rna written 8.9 years ago by User 9996 • 810 • updated 8.9 years ago by Pierre Lindenbaum ♦ 129k
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 7.5 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
8
votes
1
answer
4.5k
views
1
answer
Bedtools Intersectbed
bedtools intersect coverage written 8.7 years ago by Ian ♦ 5.7k • updated 8.7 years ago by brentp ♦ 23k
6
votes
2
answers
3.6k
views
2
answers
Intersectbed Overlap
bedtools overlap intersect written 8.7 years ago by Nicolas Rosewick ♦ 9.0k • updated 8.7 years ago by Alex Reynolds ♦ 30k
1
vote
1
answer
3.1k
views
1
answer
How To Combine Fpkm Values From Cufflinks With Contigs From De Novo Assembly Program Velvet/Oases?
bedtools cufflinks intersect velvet written 8.7 years ago by User 6181 • 0 • updated 8.7 years ago by Rlong • 340
4
votes
1
answer
2.5k
views
1
answer
Bedtools To Compare A Vcf File From Samtools Mpileup With Dbsnp?
bedtools vcf written 8.7 years ago by Deniz • 210 • updated 8.7 years ago by Swbarnes2 • 1.5k
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
13
votes
3
answers
8.9k
views
5 follow
3
answers
Multi Thread Bedtools
bedtools parallel written 8.6 years ago by Nicolas Rosewick ♦ 9.0k • updated 6.1 years ago by Biostar ♦♦ 20
3
votes
2
answers
1.4k
views
2
answers
To Group Items In Bed Files
bedtools merge written 8.6 years ago by Bioscientist • 1.7k • updated 8.6 years ago by Malachi Griffith ♦ 18k
4
votes
1
answer
3.2k
views
1
answer
How Do You Get The Quality Score And Coverage For Every Single Position Of A Reference Assembly
bedtools quality samtools coverage written 8.5 years ago by Joseph Hughes • 2.8k • updated 8.5 years ago by Pierre Lindenbaum ♦ 129k
25
votes
1
answer
22k
views
6 follow
1
answer
How To Use Bedtools To Extract Promoters From A Mouse Bed File
bedtools bed extraction promoter fasta written 8.5 years ago by Anima Mundi • 2.7k • updated 8.5 years ago by Aaronquinlan ♦ 11k
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
15
votes
1
answer
3.7k
views
1
answer
Bedtools: Top N Most Similar Regions When Comparing Two Bed/Wig/Bam Files?
bedtools correlation written 8.5 years ago by Ahdf-Lell-Kocks • 1.6k • updated 8.5 years ago by Aaronquinlan ♦ 11k
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
1
answer
1.7k
views
1
answer
Convert Bamtobed Score
bedtools scoring written 8.4 years ago by Stevelor • 310 • updated 8.3 years ago by Pascal • 1.5k
11
votes
2
answers
5.4k
views
6 follow
2
answers
Counting The Whole Insert Size From Paired-End Reads As Coverage
bedtools paired written 8.4 years ago by Alastair Kerr ♦ 5.2k • updated 8.4 years ago by Aaronquinlan ♦ 11k
8
votes
2
answers
2.9k
views
2
answers
Per Base Coverage
bedtools coverage written 8.4 years ago by Info_Nowise • 10 • updated 8.4 years ago by Aaronquinlan ♦ 11k
1
vote
1
answer
1.2k
views
1
answer
Does Bedtools Intersect -V Consider Unmapped Reads "As Not In B"
bedtools written 8.4 years ago by Jeremy Leipzig ♦ 19k • updated 8.4 years ago by Ying W • 4.0k
3
votes
2
answers
2.9k
views
2
answers
Snps Comparison
bedtools gff vcftools snp written 8.4 years ago by Ric • 160 • updated 8.4 years ago by Occam • 380
0
votes
1
answer
2.3k
views
1
answer
How To Check Whole Genome With Bigwigsummary ?
bedtools bigwig written 8.4 years ago by Ar Es • 0 • updated 6.0 years ago by Biostar ♦♦ 20
20
votes
3
answers
3.6k
views
7 follow
3
answers
How To Find The Nearest Gene To A Retrotransposon Insert?
bedtools bed position mouse written 8.4 years ago by Joseph Hughes • 2.8k • updated 8.4 years ago by Alex Reynolds ♦ 30k
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
32
votes
3
answers
8.7k
views
13 follow
3
answers
Picking Random Genomic Positions
perl bedtools bash written 8.1 years ago by PoGibas ♦ 4.8k
5
votes
1
answer
7.9k
views
1
answer
Intersectbed - Overlap Analysis Usign Vcf And Bed Files
bedtools written 8.1 years ago by Khader Shameer ♦ 18k • updated 8.1 years ago by Sukhdeep Singh ♦ 10k
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