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<prev • 541 results • page 1 of 19 • next >
6
votes
1
answer
124
views
1
answer
BWA mem of a heavily masked reference index takes more time than the normal reference?
alignment bwa written 4 days ago by Duarte Molha • 200 • updated 4 days ago by karl.stamm ♦ 3.3k
2
votes
0
answers
96
views
0
answers
Align reads on multi-fasta (contigs) file?
bwa written 5 days ago by ThePresident • 90
0
votes
1
answer
104
views
1
answer
Read group information
gatk picard read group bwa written 11 days ago by bwczech • 0 • updated 11 days ago by WouterDeCoster ♦ 30k
3
votes
2
answers
140
views
2
answers
How can I map reads only of a certain length?
atac-seq bwa sequencing written 13 days ago by a.rex • 110 • updated 13 days ago by Pierre Lindenbaum ♦ 110k
1
vote
1
answer
94
views
1
answer
Viewing the sai file generated using bwa
mapping bwa written 14 days ago by Louis Kok • 10 • updated 14 days ago by noahaus • 10
0
votes
0
answers
95
views
0
answers
BWA. Allocate memory
next-gen alignment memory bwa sequencing written 18 days ago by windsur • 0
1
vote
1
answer
121
views
1
answer
Duplicate SAMSequenceDictionary in SAM file - how to modify SAM header?
sam file bwa sequencedictionary written 21 days ago by kwalter • 10 • updated 20 days ago by finswimmer ♦ 3.6k
7
votes
1
answer
674
views
1
answer
bwa mem misaligns my contigs to the reference by a few bases
contig alignment bwa mem bwa bwt written 12 months ago by cristian • 110 • updated 21 days ago by Biostar ♦♦ 20
3
votes
1
answer
139
views
1
answer
Can someone explain what the -M option in BWA-MEM does?
alignment bwa written 25 days ago by James Reeve • 10 • updated 25 days ago by Devon Ryan ♦ 81k
11
votes
3
answers
225
views
7 follow
3
answers
Does BWA mem ever discard or modify data
bwa written 4 weeks ago by e.benn • 40
5
votes
1
answer
132
views
1
answer
How to extract aligned exactly 1 time in Single end read?
bowtie2 alignment bwa written 4 weeks ago by star • 60 • updated 4 weeks ago by zx8754 ♦ 4.6k
4
votes
0
answers
97
views
0
answers
no exact read?
R alignment chip-seq bwa bowtie2 written 4 weeks ago by star • 60
8
votes
3
answers
122
views
6 follow
3
answers
BWA (mem, sampe, or aln) used in bam file
bam bwa sequencing written 4 weeks ago by rborges • 50
3
votes
1
answer
182
views
1
answer
Why does inclusion of decoy sequences cause more BWA alignments to an autosome?
hs37d5 bwa written 7 weeks ago by pamela.russell.ucdenver • 20
1
vote
0
answers
149
views
0
answers
extracting orphan reads from bam file
bam file samtools bwa orphan reads sa flag written 8 weeks ago by Assa Yeroslaviz • 1.1k
1
vote
1
answer
126
views
1
answer
problem for setting BWA arguments for alignment
alignment rna-seq bwa sequencing written 8 weeks ago by modarzi • 20 • updated 8 weeks ago by toralmanvar • 420
0
votes
0
answers
135
views
0
answers
Trying to get consensus sequence from paired end alignment
paired-end alignment samtools bwa written 9 weeks ago by Sus • 0
3
votes
0
answers
130
views
0
answers
Benchmarking single SNP mapping
snps bowtie wgsim bwa mapping written 11 weeks ago by Josh Herr ♦ 5.5k • updated 9 weeks ago by Biostar ♦♦ 20
3
votes
1
answer
185
views
1
answer
QC-passed reads in BWA aln and BWA mem
alignment bwa mem bwa qc-passed bwa aln written 10 weeks ago by kaiho • 10 • updated 10 weeks ago by swbarnes2 ♦ 3.8k
0
votes
1
answer
202
views
1
answer
Peak calling with MACS for paired end DNase-seq data
macs2 paired-end dna-seq bwa written 10 weeks ago by Bioinformatist Newbie • 230 • updated 10 weeks ago by igor ♦ 6.3k
4
votes
1
answer
1.7k
views
1
answer
Why there is huge difference in mapping quality with bwa & bowtie
next-gen alignment samtools bwa bowtie written 3.5 years ago by Govardhan Anande • 130 • updated 10 weeks ago by Biostar ♦♦ 20
0
votes
1
answer
158
views
1
answer
How to unique bwa mem reads?
unique reads bwa single cell atac-seq written 11 weeks ago by niu.shengyong • 30
0
votes
1
answer
111
views
1
answer
getting bwa to ignore some parts of a read
illumina bwa written 11 weeks ago by Fedster • 0 • updated 11 weeks ago by swbarnes2 ♦ 3.8k
5
votes
2
answers
169
views
2
answers
mapping form different lane
ngs bwa written 11 weeks ago by siyavash_damdar • 20 • updated 11 weeks ago by swbarnes2 ♦ 3.8k
2
votes
1
answer
185
views
5 follow
1
answer
Are there any GNU parallel or similar Shell/Bash code examples on how to run Snap and BWA aligners on a batch of paired .fastq files?
snap parallel shell gnu bwa written 12 weeks ago by england_bioinformatics_team • 10 • updated 12 weeks ago by ATpoint • 5.5k
4
votes
2
answers
1.1k
views
2
answers
bwa mem: Passing a variable to read group
variant calling bwa-mem alignment bwa gatk written 8 months ago by rmf • 280
0
votes
1
answer
854
views
1
answer
BWA shm index preloading: only for BWA MEM?
hengli bwa written 23 months ago by Maximilian Haeussler • 1.3k
8
votes
2
answers
8.4k
views
8 follow
2
answers
Soft-Clipped Vs Unmapped?
bwa written 6.3 years ago by Bioscientist • 1.6k • updated 3 months ago by fatima.m.zare • 20
3
votes
1
answer
183
views
1
answer
increase BWA sensitivity
metagenomics bwa hg19 written 3 months ago by sacha • 1.3k • updated 3 months ago by h.mon ♦ 16k
13
votes
3
answers
397
views
3
answers
Number of threads in BWA
ngs alignment bwa written 3 months ago by siyavash_damdar • 20 • updated 3 months ago by d-cameron • 1.8k
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