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3
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0
answers
882
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bwa mem -R (RGline) format for DNBseq fastq
wgs dnbseq bwa mem fastq bwa written 13 months ago by joe • 140 • updated 17 days ago by xxa • 0
0
votes
1
answer
159
views
1
answer
BWA aligning forward and reverse differently
bwa mem written 5 weeks ago by dorothea.emig • 0 • updated 5 weeks ago by h.mon ♦ 31k
0
votes
0
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138
views
0
answers
BWA mem paired end read name errors
paired end reads bwa mem bwa written 11 weeks ago by dp • 40
3
votes
1
answer
599
views
5 follow
1
answer
How does BWA MEM know where to put X and Y origin reads correctly?
bwa mem alignment genetics genomics written 17 months ago by s1667153 • 0 • updated 17 months ago by WouterDeCoster ♦ 44k
0
votes
1
answer
396
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1
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Should I use the same reference indexing command of bwa for WGS and WES analysis?
indexing wes bwa mem wgs written 18 months ago by maria2019 • 100 • updated 18 months ago by finswimmer ♦ 13k
1
vote
1
answer
505
views
5 follow
1
answer
bwa mem low depth and fluctuating plot
bwa mem samtools written 2.0 years ago by ieie • 10 • updated 2.0 years ago by singh.vijender • 30
0
votes
0
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752
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0
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bwa mem cannot locate output bam file
bwa mem rna-seq written 2.1 years ago by alexadeanfitz • 10 • updated 2.1 years ago by ATpoint ♦ 39k
1
vote
1
answer
819
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1
answer
illumina data analysis with bwa mem
bwa mem written 2.2 years ago by bioguy24 • 190 • updated 2.2 years ago by Devon Ryan ♦ 96k
8
votes
1
answer
1.8k
views
1
answer
bwa mem misaligns my contigs to the reference by a few bases
contig alignment bwa mem bwa bwt written 3.2 years ago by cristian • 240 • updated 2.3 years ago by Biostar ♦♦ 20
3
votes
1
answer
1.1k
views
1
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QC-passed reads in BWA aln and BWA mem
alignment bwa mem bwa qc-passed bwa aln written 2.4 years ago by kai • 10 • updated 2.4 years ago by swbarnes2 ♦ 8.7k
3
votes
1
answer
2.0k
views
1
answer
Does BWA mem work with uBAM file?
ubam bwa mem bwa align written 2.6 years ago by Abdul Rafay Khan • 1.1k
15
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0
answers
1.1k
views
5 follow
0
answers
Penalty model of BWA MEM and BOWTIE2?
bowtie2 alignment bwa mem rna-seq written 2.7 years ago by John • 210
22
votes
4
answers
5.7k
views
10 follow
4
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Aligning paired end fastq files dumped from SRA
sra fastq bwa mem paired written 5.9 years ago by Zev.Kronenberg ♦ 11k • updated 2.8 years ago by seelament • 0
2
votes
1
answer
992
views
1
answer
Mapping Illumina reads using BWA
assembly bwa mem mapping bwa sequencing written 2.8 years ago by James • 20 • updated 2.8 years ago by h.mon ♦ 31k
18
votes
3
answers
2.6k
views
3
answers
Lack of consensus between NGS & Sanger sequencing on indels/mutations
indel sanger ngs bwa mem variant calling written 4.9 years ago by alons • 270 • updated 2.9 years ago by Kevin Blighe ♦ 66k
3
votes
0
answers
2.0k
views
0
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bwa mem segfault
segfault bwa mem bwa written 3.0 years ago by lindsay.liang • 20
13
votes
1
answer
888
views
5 follow
1
answer
Is my file created completely
sam file bwa mem written 3.4 years ago by micro32uvas • 10 • updated 3.4 years ago by h.mon ♦ 31k
11
votes
1
answer
2.4k
views
9 follow
1
answer
Oxford Nanopore BWA MEM alignments
long reads bwa mem bwa oxford nanopore written 3.4 years ago by QVINTVS_FABIVS_MAXIMVS • 2.4k • updated 3.4 years ago by WouterDeCoster ♦ 44k
11
votes
3
answers
3.1k
views
3
answers
BWA mem output inconsistent on same but re-ordered FASTQ input
assembly alignment bwa mem tool bwa written 3.6 years ago by ramy • 10
0
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0
answers
3.9k
views
0
answers
Mismatch setting for bwa mem ?
bwa mem mismatch written 3.7 years ago by Picasa • 560
4
votes
1
answer
1.4k
views
1
answer
Weird issue with bam file generated by samtools
samtools bam bwa mem written 3.7 years ago by lakhujanivijay ♦ 5.2k • updated 3.7 years ago by Devon Ryan ♦ 96k
1
vote
0
answers
1.4k
views
0
answers
BWA option for FR sens only
bwa mem written 3.8 years ago by Picasa • 560
2
votes
1
answer
1.3k
views
1
answer
paired reads (headers) show up in 3 lines of sam file instead of expected 2
alignment bwa mem sam written 4.2 years ago by raplayer • 10 • updated 4.2 years ago by Damian Kao ♦ 15k
4
votes
2
answers
1.9k
views
2
answers
How to identify the chromosome where the reads has the secondary (alternative alignments), after running bwa mem?
alignment bwa mem sam bam written 4.3 years ago by kirannbishwa01 • 1.2k • updated 4.3 years ago by dariober ♦ 11k
4
votes
1
answer
1.7k
views
1
answer
insert size discrepencies using bwa backtrack and bwa mem
bwa-backtrack bwa mem insert written 4.3 years ago by urmi208 • 30 • updated 4.3 years ago by lh3 ♦ 32k
3
votes
1
answer
3.4k
views
1
answer
calling BWA mem from within python
python bwa mem written 4.4 years ago by lien • 90 • updated 4.4 years ago by Picasa • 560
2
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0
answers
2.0k
views
0
answers
parameters in bwa mem
parameters tools bwa mem bwa written 4.7 years ago by BioinfoNovice • 110
6
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0
answers
3.1k
views
0
answers
Tool: Wham - a structural variant caller and association testing framework
gwas tool structural variant bam bwa mem genotype written 5.7 years ago by Zev.Kronenberg ♦ 11k
43
votes
1
answer
32k
views
22 follow
1
answer
When and why is bwa aln better then bwa mem?
comparison bwa mem bwa aln written 5.9 years ago by dariober ♦ 11k • updated 5.9 years ago by Istvan Albert ♦♦ 85k
1
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0
answers
4.6k
views
0
answers
bwa mem mismatch option
bwa mem written 6.0 years ago by Varun Gupta • 1.2k
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