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<prev • 618 results • page 1 of 21 • next >
119
votes
8
answers
59k
views
80 follow
8
answers
Tutorial: Piping With Samtools, Bwa And Bedtools
bedtools tutorial samtools unix bwa written 8.9 years ago by Ying W • 4.0k • updated 5.3 years ago by Yaseen Ladak • 30
54
votes
10
answers
8.0k
views
9 follow
10
answers
Tool: Bedtools: Analyzing Genomic Features
bedtools tool written 8.9 years ago by Istvan Albert ♦♦ 86k • updated 6.2 years ago by Aaronquinlan ♦ 11k
90
votes
3
answers
55k
views
35 follow
3
answers
Bedtools Compare Multiple Bed Files?
bedtools intersect written 9.4 years ago by Bioscientist • 1.7k • updated 8.1 years ago by sjneph • 620
14
votes
1
answer
2.2k
views
8 follow
1
answer
Tutorial: Introduction to bedtools.
bedtools tutorial written 6.3 years ago by Aaronquinlan ♦ 11k • updated 4.3 years ago by mcc • 80
36
votes
6
answers
12k
views
19 follow
6
answers
Annotating Genomic Intervals
bedtools annotation bioconductor R written 8.4 years ago by Stephen ♦ 2.8k • updated 8.4 years ago by Alex Reynolds ♦ 31k
11
votes
0
answers
5.8k
views
0
answers
Tutorial: Plot average methylation levels across TSS region
bedtools R tutorial methylation rrbs written 6.1 years ago by TriS • 4.3k • updated 6.1 years ago by Gjain ♦ 5.6k
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 8.0 years ago by user • 870 • updated 18 months ago by ATpoint ♦ 46k
32
votes
3
answers
9.2k
views
13 follow
3
answers
Picking Random Genomic Positions
perl bedtools bash written 8.7 years ago by PoGibas ♦ 4.9k
32
votes
4
answers
14k
views
17 follow
4
answers
Getting Unmapped Reads: Comparing Fastq To Bam
bedtools fastq bam samtools written 9.2 years ago by User 9996 • 810 • updated 9.2 years ago by brentp ♦ 23k
23
votes
2
answers
8.3k
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 8.0 years ago by Nick Crawford • 210
18
votes
3
answers
11k
views
13 follow
3
answers
Heatmap Of Read Coverage Around Tsss
bedtools coverage heatmap written 7.5 years ago by A. Domingues • 2.4k • updated 7.5 years ago by Ying W • 4.0k
27
votes
1
answer
24k
views
6 follow
1
answer
How To Use Bedtools To Extract Promoters From A Mouse Bed File
bedtools bed extraction promoter fasta written 9.1 years ago by Anima Mundi • 2.8k • updated 9.1 years ago by Aaronquinlan ♦ 11k
28
votes
3
answers
6.4k
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 9.1 years ago by Sander Timmer • 700 • updated 9.1 years ago by David Langenberger ♦ 9.6k
15
votes
2
answers
8.7k
views
2
answers
Reproduce Encode/Cshl Long Rna-Seq Data Visualization Viewed In Ucsc, But Failed? [Done]
bedtools encode visualization rna-seq written 8.4 years ago by Puriney • 330 • updated 8.4 years ago by Malachi Griffith ♦ 18k
18
votes
5
answers
14k
views
14 follow
5
answers
Discrepancy In Samtools Mpileup/Depth And Bedtools Genomecoveragebed Counts
bedtools samtools written 7.9 years ago by Surya Saha • 260 • updated 7.3 years ago by plafdesigns • 40
12
votes
1
answer
4.1k
views
1
answer
How to find intron co-ordinates from the gff file?
bedtools gff open intron written 5.3 years ago by Chirag Parsania • 1.9k • updated 5.3 years ago by Devon Ryan ♦ 98k
16
votes
1
answer
3.0k
views
1
answer
Bedtools sortBed | uniq and bash sort | uniq returns different number of lines
bedtools bed sort uniq bash written 4.7 years ago by QVINTVS_FABIVS_MAXIMVS • 2.4k • updated 4.7 years ago by ATpoint ♦ 46k
15
votes
1
answer
3.8k
views
1
answer
Bedtools: Top N Most Similar Regions When Comparing Two Bed/Wig/Bam Files?
bedtools correlation written 9.1 years ago by Ahdf-Lell-Kocks • 1.6k • updated 9.1 years ago by Aaronquinlan ♦ 11k
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 8.9 years ago by Joseph Hughes • 2.9k • updated 8.9 years ago by Alex Reynolds ♦ 31k
17
votes
2
answers
4.6k
views
6 follow
2
answers
Does Bedops Have A Command Similar To The Bedtools Makewindows?
bedtools written 8.1 years ago by Irsan • 7.3k • updated 6.1 years ago by Alex Reynolds ♦ 31k
32
votes
5
answers
27k
views
17 follow
5
answers
Bedtools Genomecoveragebed Usage : How To Create A Genome File?
bedtools written 7.8 years ago by komal.rathi • 3.7k • updated 16 months ago by Phoenix Mu • 40
15
votes
3
answers
3.9k
views
6 follow
3
answers
Bed File Of Mapq Sliding Window On A Bam File?
bedtools bed bam written 7.0 years ago by 14134125465346445 • 3.5k
17
votes
5
answers
8.6k
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 7.8 years ago by Malachi Griffith ♦ 18k • updated 2.3 years ago by Paul • 1.4k
10
votes
3
answers
3.6k
views
5 follow
3
answers
How To Explain Uneven Coverage Of A Dna Seqment Obtained Via Pcr Amplification.
bedtools coverage written 6.9 years ago by rohan • 100 • updated 6.7 years ago by swbarnes2 ♦ 9.6k
8
votes
2
answers
5.0k
views
2
answers
bedtools genomecov .genome file usage
bedtools genomecov written 6.0 years ago by kaston • 40
22
votes
1
answer
5.1k
views
1
answer
calling bedtools from R
bedtools R written 5.9 years ago by yasjas • 70 • updated 5.9 years ago by Irsan • 7.3k
11
votes
2
answers
8.1k
views
2
answers
Issue with naming convention in bedtools
bedtools sam written 5.9 years ago by A. Domingues • 2.4k • updated 13 months ago by Biostar ♦♦ 20
9
votes
2
answers
9.3k
views
2
answers
Can't convert paired end BAM to bed using bedtools
bedtools alignment bam written 5.7 years ago by colin.kern • 950 • updated 5.5 years ago by guillermofernandeznegrete • 0
5
votes
1
answer
2.6k
views
7 follow
1
answer
Tutorial: bam2rpkm by bedtools
bedtools rpkm tutorial bam rna-seq written 3.4 years ago by jmzeng1314 • 110 • updated 3 months ago by ATpoint ♦ 46k
5
votes
2
answers
6.6k
views
2
answers
Correlation Of Fpkm And Length Normalized Transcript Mapped Read Count
bedtools cufflinks next-gen written 8.5 years ago by johannes.helmuth • 110 • updated 2.5 years ago by Biostar ♦♦ 20
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