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32 results • Page
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Showing top results for tag:
mapq
•
reset
0
votes
2
replies
507
views
Calculation of per-base average Quality (MAPQ, basecall quality Q20) from BAMs across multiple samples
MAPQ
BAM
coverage
4 weeks ago by
Novice
▴ 10
1
vote
3
replies
343
views
Why is one mate not in proper pair in one case, when it is in proper pair in a very similar case?
bwa-mem
alignment
mapq
updated 3 months ago by
Istvan Albert
101k • written 3 months ago by
fesokaw279
• 0
0
votes
3
replies
3.3k
views
minimap's SAM file MAPQ value for the unique alignments
minimap
MAPQ
RNAseq
17 months ago by
Mo
▴ 50
18
votes
9
replies
4.1k
views
MAPQ filtering for clinical applications
MAPQ
clinical NGS
updated 17 months ago by
DKA
▴ 40 • written 7.1 years ago by
Kevin Blighe
88k
4
votes
1
reply
844
views
Why some reads have MAPQ = 0 with bwa and look good?
alignment
mapq
bwa
maping
updated 22 months ago by
acvill
▴ 350 • written 22 months ago by
lacb
▴ 120
2
votes
2
replies
861
views
bowtie2 MAPQ scores more than 42
MAPQ
bowtie2
2.5 years ago by
rakusmaximus
• 0
2
votes
3
replies
1.2k
views
Get the coverage after read alignment with bwa-mem2
coverage
alignment
bwa-mem2
MAPQ
updated 2.5 years ago by
Pappu
★ 2.1k • written 2.5 years ago by
maxime.policarpo
▴ 200
0
votes
0
replies
382
views
Mapq filtered bigwigs have higher peaks than unfiltered bigwigs?
bigwig
normalization
deeptools
mapq
updated 16 months ago by
Ram
44k • written 2.6 years ago by
Megan
• 0
0
votes
1
reply
1.3k
views
bbmap, mapq and uniquelly mapped reads filtering
alignment
mapq
updated 3.6 years ago by
GenoMax
146k • written 3.6 years ago by
boczniak767
▴ 870
2
votes
2
replies
1.9k
views
Can BWA-MEM MAPQ Score = 70?
Phred
BWA-MEM
MAPQ
software error
updated 4.1 years ago by
Istvan Albert
101k • written 4.1 years ago by
Saha.Neiladri
• 0
4
votes
7
replies
1.1k
views
Reads mapped with zero quality still mapped to exactly one position
bwa
mapping quality
mapq
mq
updated 4.2 years ago by
Istvan Albert
101k • written 4.2 years ago by
bataloffv
▴ 20
4
votes
6
replies
3.3k
views
Is MAPQ score related to Phred quality score?
MAPQ
Phred quality score
updated 4.3 years ago by
Jeremy Leipzig
22k • written 4.3 years ago by
dpc
▴ 250
2
votes
3
replies
946
views
BWA Aln Quality of 0 for perfect match read ?
alignment
bwa
bwa aln
MapQ
4.9 years ago by
ADDNOTHIING
▴ 10
1
vote
3
replies
1.0k
views
How does base quality / mapping quality affect germline calling
haplotypecaller
germline calling
MAPQ
5.1 years ago by
CY
▴ 750
1
vote
3
replies
1.0k
views
.bam mpileup mapping quality
mpileup
samtools
sanger FASTQ
MAPQ
updated 5.1 years ago by
jkbonfield
★ 1.3k • written 5.1 years ago by
saar.armon
• 0
10
votes
14
replies
11k
views
Is there a way to do read filtering (MAPQ> certain value) on a BAM instead of SAM file?
BAM
SAM
MAPQ
quality
filtering
5.8 years ago by
msimmer92
▴ 310
0
votes
1
reply
2.3k
views
mpileup mapping quality
samtools
MAPQ
updated 6.3 years ago by
Kevin Blighe
88k • written 6.3 years ago by
hpapoli
▴ 150
4
votes
1
reply
5.6k
views
BWA-mem MAPQ Calculation
BWA-mem
mapq
mq
mapping quality
alignment
updated 6.3 years ago by
h.mon
35k • written 8.3 years ago by
rfriedman22
▴ 40
1
vote
1
reply
3.6k
views
difference between mapq=0 and samtools flag 0x900
samtools
mapq
updated 6.4 years ago by
Devon Ryan
104k • written 6.4 years ago by
bitpir
▴ 250
1
vote
1
reply
2.5k
views
bowtie2 : different MAPQ if -k is set
bowtie2
mapq
updated 7.0 years ago by
h.mon
35k • written 7.0 years ago by
Nicolas Rosewick
11k
3
votes
2
replies
2.5k
views
Mapping Quality of reads with mismatches in STAR
STAR
RNAseq
MAPQ
updated 7.3 years ago by
Devon Ryan
104k • written 7.3 years ago by
grant.hovhannisyan
★ 2.6k
1
vote
1
reply
2.9k
views
Structural Variation Discovery: Delly's Output
sv
delly
mapq
updated 7.3 years ago by
trausch
★ 1.9k • written 7.7 years ago by
novice
★ 1.1k
3
votes
6
replies
2.6k
views
Increase the fifth column ( MAPQ) value in Sam file
sam
MAPQ
sequencing
alignment
updated 7.4 years ago by
novice
★ 1.1k • written 7.4 years ago by
madhu.9124
▴ 60
5
votes
11
replies
3.8k
views
All reads with mapq value <= 1, htseq does not attribute counts to any feature
rnaseq
mapq
8.6 years ago by
fhsantanna
▴ 620
2
votes
3
replies
4.3k
views
How can I best use -c in bwa mem for alignment and to find polymorphisms?
SNP
bwa
mapQ
sequencing
alignment
updated 2.3 years ago by
Ram
44k • written 8.7 years ago by
kirannbishwa01
★ 1.6k
5
votes
9
replies
3.5k
views
Why the file unmapped.bam, from tophat has all reads with mapq =/> 30?
samstat
tophat
mapq
updated 2.1 years ago by
Ram
44k • written 9.2 years ago by
tiago211287
★ 1.5k
2
votes
3
replies
4.0k
views
Genotyping from RNA-Seq: how to recalibrate mapping quality scores in BAM file?
recalibrate
STAR
bam
mapq
RNA-Seq
updated 23 months ago by
Ram
44k • written 9.3 years ago by
Leszek
4.2k
0
votes
1
reply
4.1k
views
bwa-0.7.12 AS:i and XS:i match but MAPQ = 0
MAPQ
bwa
updated 2.4 years ago by
Ram
44k • written 9.6 years ago by
suzanne.mcgaugh
▴ 60
4
votes
7
replies
3.1k
views
reads mapped in proper pair (99/147) but mapq=0 ?
mapq
bam
read
updated 2.7 years ago by
Ram
44k • written 9.9 years ago by
Pierre Lindenbaum
164k
1
vote
1
reply
3.3k
views
RNA-seq reads mapping to paralogs with high MAPQ. How to ensure this?
paralogs
BWA
RNA-Seq
MAPQ
updated 2.7 years ago by
Ram
44k • written 10.0 years ago by
biotech
▴ 570
2
votes
3
replies
3.8k
views
Is correct finding unique reads with the flag -F 0x104?
bwa
RNA-Seq
bowtie2
mapq
flag
updated 2.9 years ago by
Ram
44k • written 10.3 years ago by
miquinhap
• 0
2
votes
4
replies
4.6k
views
How to compute MAPQ distribution with Rsamtools
MAPQ
Rsamtools
BAM
updated 3.1 years ago by
Ram
44k • written 10.5 years ago by
Nicola Casiraghi
▴ 500
32 results • Page
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