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<prev • 462 results • page 1 of 16 • next >
54
votes
10
answers
6.9k
views
9 follow
10
answers
Tool: Bedtools: Analyzing Genomic Features
bedtools tool written 6.6 years ago by Istvan Albert ♦♦ 78k • updated 3.9 years ago by Aaronquinlan ♦ 10k
109
votes
10
answers
46k
views
75 follow
10
answers
Tutorial: Piping With Samtools, Bwa And Bedtools
bedtools tutorial samtools unix bwa written 6.6 years ago by Ying W • 3.9k • updated 3.1 years ago by Yaseen Ladak • 20
9
votes
7
answers
3.5k
views
6 follow
7
answers
randomly shuffle BAM file
bedtools bam shuffle written 3.4 years ago by mparker2 • 20 • updated 19 months ago by skanterakis • 80
6
votes
6
answers
13k
views
8 follow
6
answers
How Can I Compare And Merge Bed Files
bedtools bed written 6.4 years ago by lyfsa • 30 • updated 5.6 years ago by beary.pooh • 10
32
votes
6
answers
9.7k
views
14 follow
6
answers
Annotating Genomic Intervals
bedtools annotation bioconductor R written 6.2 years ago by Stephen ♦ 2.6k • updated 6.2 years ago by Alex Reynolds ♦ 26k
17
votes
5
answers
12k
views
13 follow
5
answers
Discrepancy In Samtools Mpileup/Depth And Bedtools Genomecoveragebed Counts
bedtools samtools written 5.7 years ago by Surya Saha • 250 • updated 5.1 years ago by plafdesigns • 30
17
votes
5
answers
7.0k
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 5.6 years ago by Malachi Griffith ♦ 17k • updated 5 weeks ago by Paul • 1.2k
2
votes
5
answers
326
views
6 follow
5
answers
Expanding Genomic Coordinates Using Bedtools
bedtools bed tools genomc bed file written 5 months ago by gtasource • 20 • updated 5 months ago by Aaronquinlan ♦ 10k
6
votes
5
answers
358
views
5 follow
5
answers
Extract start coordinate from read 1 and end coordinate from read 2 of paired end reads.
bedtools unix written 3 months ago by rjobmc • 0 • updated 3 months ago by finswimmer ♦ 7.8k
7
votes
5
answers
126
views
5 follow
5
answers
Pulling out interval adjoining regions
bedtools bed bedops interval written 13 days ago by rbronste • 230 • updated 12 days ago by Alex Reynolds ♦ 26k
31
votes
4
answers
13k
views
15 follow
4
answers
Getting Unmapped Reads: Comparing Fastq To Bam
bedtools fastq bam samtools written 7.0 years ago by User 9996 • 790 • updated 7.0 years ago by brentp ♦ 22k
3
votes
4
answers
8.8k
views
5 follow
4
answers
Genomecoveragebed - Bedtool For Reporting Per Base Genome Coverage
bedtools coverage written 6.8 years ago by Varun Gupta • 1.1k • updated 4.9 years ago by hygine555 • 0
4
votes
4
answers
3.1k
views
6 follow
4
answers
Extract Only Paired-End Reads That Map A Specific Interval
bedtools extraction written 6.3 years ago by Nicolas Rosewick ♦ 7.0k • updated 8 weeks ago by pnatsidis • 0
5
votes
4
answers
4.2k
views
5 follow
4
answers
N Closest Genes To A Given Location
bedtools intersect written 6.2 years ago by dfernan • 640 • updated 6.2 years ago by Alex Reynolds ♦ 26k
30
votes
4
answers
23k
views
16 follow
4
answers
Converting Bam To Bedgraph For Viewing On Ucsc?
bedtools bed bam genome-browser ucsc written 5.8 years ago by user • 780 • updated 5 months ago by ATpoint ♦ 10k
17
votes
4
answers
19k
views
12 follow
4
answers
Bedtools Genomecoveragebed Usage : How To Create A Genome File?
bedtools written 5.6 years ago by komal.rathi • 3.3k • updated 9 weeks ago by Medhat ♦ 8.0k
5
votes
4
answers
1.8k
views
5 follow
4
answers
Tool For Binning Windowbed Output For K-Means Clustering
bedtools chip-seq clustering heatmap written 5.2 years ago by bede.portz • 470
1
vote
4
answers
4.0k
views
5 follow
4
answers
To Calculate The Exact Total Number Of Mapped Reads In Exome Regions
bedtools gatk ngs exome-sequencing coverage written 5.0 years ago by vchris_ngs • 4.6k • updated 5.0 years ago by Wei Shi • 0
13
votes
4
answers
4.8k
views
5 follow
4
answers
Calculating GC content from BAM file by BED file
cg content bed bam bedtools written 4.0 years ago by Paul • 1.2k • updated 4.0 years ago by Aaronquinlan ♦ 10k
3
votes
4
answers
3.7k
views
4
answers
Intersect multiple bed and keep all fields
bedtools bed bedops written 3.4 years ago by user230613 • 260 • updated 13 months ago by ashmc • 0
1
vote
4
answers
720
views
4
answers
Generate bed co-ordinates other then given input bed file
bedfile bedtools written 2.6 years ago by Chirag Parsania • 1.2k • updated 2.5 years ago by A. Domingues • 1.7k
0
votes
4
answers
952
views
4
answers
condition bedtools on name column
bedtools written 2.4 years ago by burnsro • 20 • updated 2.4 years ago by Alex Reynolds ♦ 26k
12
votes
4
answers
4.9k
views
9 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 22 months ago by tara.alpert • 30 • updated 11 months ago by brianpenghe • 0
5
votes
4
answers
500
views
4
answers
bedtools - getfasta: How to report both 'chrom:start-stop and' 'name' of sequence?
bedtools written 7 months ago by bi_Scholar • 0 • updated 7 months ago by Alex Reynolds ♦ 26k
7
votes
3
answers
6.8k
views
5 follow
3
answers
Convert .Txt Into Bed Files
bedtools comparison written 7.4 years ago by Bioscientist • 1.6k • updated 7.4 years ago by Swbarnes2 • 1.4k
76
votes
3
answers
40k
views
29 follow
3
answers
Bedtools Compare Multiple Bed Files?
bedtools intersect written 7.1 years ago by Bioscientist • 1.6k • updated 5.9 years ago by sjneph • 600
7
votes
3
answers
4.9k
views
5 follow
3
answers
Reporting The Bam Reads Overlapping A Set Of Intervals With Bedtools
bedtools bed next-gen bam sequencing written 7.1 years ago by User 9996 • 790 • updated 7.1 years ago by Alex Reynolds ♦ 26k
11
votes
3
answers
6.1k
views
5 follow
3
answers
Multi Thread Bedtools
bedtools parallel written 7.0 years ago by Nicolas Rosewick ♦ 7.0k • updated 4.4 years ago by Biostar ♦♦ 20
28
votes
3
answers
5.5k
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 6.8 years ago by Sander Timmer • 700 • updated 6.8 years ago by David Langenberger ♦ 8.4k
18
votes
3
answers
3.2k
views
6 follow
3
answers
How To Find The Nearest Gene To A Retrotransposon Insert?
bedtools bed position mouse written 6.7 years ago by Joseph Hughes • 2.6k • updated 6.7 years ago by Alex Reynolds ♦ 26k
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