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15
votes
6
answers
5.3k
views
13 follow
6
answers
bedtools coverage gives error received illegal bin number, but that number isn't in my data!
bedtools bin chip-seq coverage error written 23 months ago by tara.alpert • 30 • updated 1 day ago by pangxy3 • 0
1
vote
0
answers
85
views
0
answers
What coverage is recommended for amplicon sequencing?
amplicon coverage written 4 days ago by Picasa • 390
0
votes
1
answer
108
views
1
answer
How to conclude in a significant decrease of coverage depth
genome alignment next-gen samtools coverage written 19 days ago by maxime.policarpo • 40 • updated 18 days ago by Ahill • 1.3k
0
votes
1
answer
112
views
1
answer
Lower Assembly Quality Despite Higher Coverage?
genome assembly next-gen coverage alignment written 21 days ago by GTR • 0 • updated 21 days ago by h.mon ♦ 22k
9
votes
2
answers
124
views
2
answers
What would be the expected average coverage of a 384 multiplexed run on a Novaseq S4 flowcell?
novaseq coverage written 7 weeks ago by Biomed ♦ 4.4k • updated 7 weeks ago by ATpoint ♦ 12k
4
votes
1
answer
436
views
1
answer
Giga base or Giga byte
gb assembly coverage written 5 months ago by Shawrob400 • 10 • updated 7 weeks ago by ATpoint ♦ 12k
5
votes
1
answer
159
views
1
answer
Finding out which genes are covered the most
genes coverage written 8 weeks ago by shubhra.bhattacharya • 120 • updated 8 weeks ago by Pierre Lindenbaum ♦ 116k
0
votes
0
answers
138
views
0
answers
Is is possible to find "SureSelectXT Human Methyl-Seq Capture Library" somewhere?
methyl-seq capture library ssmethylseq coverage written 3 months ago by daisy.ko • 20 • updated 9 weeks ago by Biostar ♦♦ 20
7
votes
3
answers
4.2k
views
3
answers
How do I access genome coverage using SPADES?
genome spades coverage myposts written 3.4 years ago by fhsantanna • 430 • updated 9 weeks ago by DK • 70
6
votes
2
answers
205
views
2
answers
find coverage of specific exomes from a bam file
bedtools genomecov bam coverage bed written 10 weeks ago by lait • 120 • updated 10 weeks ago by Pierre Lindenbaum ♦ 116k
0
votes
0
answers
128
views
0
answers
how can I get the coverage over introns only in a RNA-seq experiment?
introns coverage rna-seq written 10 weeks ago by Lila M • 410
8
votes
1
answer
484
views
5 follow
1
answer
Is there any precedent for considering marked duplicates when calculating coverage in high-depth whole-exome sequencing?
exome duplicates exome-seq coverage written 8 months ago by Dan D ♦ 6.7k • updated 11 weeks ago by marco_ul • 0
4
votes
2
answers
192
views
2
answers
coverage of a SNP site?
bedtools ngs ase coverage snp written 11 weeks ago by Susmita Mandal • 20 • updated 11 weeks ago by Kevin Blighe ♦ 35k
17
votes
5
answers
7.1k
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 5.7 years ago by Malachi Griffith ♦ 17k • updated 11 weeks ago by Paul • 1.2k
0
votes
0
answers
861
views
0
answers
Rtracklayer: Converting rlelist (Coverage) to bigwig
rtracklayer bigwig coverage written 2.3 years ago by datascientist28 • 350 • updated 11 weeks ago by Biostar ♦♦ 20
2
votes
1
answer
147
views
1
answer
What sequence has being read by IGV's 'copy sequence'
igv alignment samtools coverage read map written 12 weeks ago by marongiu.luigi • 350 • updated 12 weeks ago by h.mon ♦ 22k
0
votes
1
answer
136
views
1
answer
Is BED file generated by bametobed sorted ?
bedtools ngs bamtobed coverage sequencing written 3 months ago by pacman • 50 • updated 3 months ago by Alex Reynolds ♦ 27k
0
votes
2
answers
2.0k
views
2
answers
Mapping Reads Back To Assembly Contigs To Generate Pileup
pileup bwa coverage written 6.8 years ago by Sen • 0 • updated 4 months ago by Biostar ♦♦ 20
0
votes
0
answers
195
views
0
answers
Calculating breadth of coverage for TCGA Whole Exome Sequencing data
tcga coverage written 4 months ago by steve • 1.9k
2
votes
0
answers
1.4k
views
0
answers
coverage in amplicon sequecing method
coverage written 2.9 years ago by Picasa • 390 • updated 4 months ago by RamRS ♦ 20k
2
votes
0
answers
1.0k
views
0
answers
I have some queries on coverage
rnaseq dnaseq coverage snp written 2.9 years ago by bioinforesearchquestions • 190 • updated 4 months ago by RamRS ♦ 20k
8
votes
2
answers
270
views
5 follow
2
answers
Good mean coverage but big std in coverage
bamqc rnaseq qualimap coverage written 4 months ago by Pin.Bioinf • 220
1
vote
2
answers
231
views
2
answers
what is the conventional apporach to calculate depth of coverage?
wgs dnaseq coverage snp depth written 4 months ago by serpalma.v • 20 • updated 4 months ago by finswimmer ♦ 9.0k
24
votes
1
answer
12k
views
1
answer
samtools bedcov vs. bedtools coverage
dna-seq coverage written 2.6 years ago by Dataman • 260 • updated 4 months ago by RamRS ♦ 20k
7
votes
4
answers
1.6k
views
5 follow
4
answers
Confirming Structural Variants In The Genome
genome coverage written 6.6 years ago by Rubal7 • 720 • updated 5 months ago by Biostar ♦♦ 20
227
votes
11
answers
131k
views
108 follow
11
answers
Tools To Calculate Average Coverage For A Bam File?
bam coverage sequencing written 8.0 years ago by Biomed ♦ 4.4k • updated 5 months ago by WouterDeCoster ♦ 36k
11
votes
3
answers
4.0k
views
10 follow
3
answers
Visualizing Coverage Of Ngs Reads Across Reference Genome
coverage sequencing written 5.5 years ago by nicolazilio • 20 • updated 5 months ago by Biostar ♦♦ 20
11
votes
4
answers
4.0k
views
4
answers
Calculate percentage of bases covered less than nX in targeted sequencing experiment
ngs coverage targeted sequencing written 4.0 years ago by RamRS ♦ 20k • updated 5 months ago by toni • 2.1k
1
vote
1
answer
410
views
1
answer
relationship between DP and variant call quality
read depth variant quality coverage dp written 6 months ago by miaowzai • 110 • updated 6 months ago by finswimmer ♦ 9.0k
1
vote
0
answers
249
views
0
answers
Extract the overlap of well-covered regions across multiple samples
wgs coverage written 6 months ago by DVA • 490
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