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4
votes
1
answer
230
views
1
answer
Reads mapped with zero quality still mapped to exactly one position
mq mapping quality mapq bwa written 5 months ago by bataloffv • 20 • updated 5 months ago by Istvan Albert ♦♦ 86k
0
votes
0
answers
224
views
0
answers
Alignment of reads to gene and pseudogene
gene pseudogene alignment mapping quality bwa written 6 months ago by nkausthu • 30
3
votes
1
answer
2.6k
views
1
answer
Remove both pair end reads with low mapping quality using Samtools
mapping quality samtools written 6.2 years ago by DVA • 550 • updated 11 months ago by Biostar ♦♦ 20
1
vote
0
answers
789
views
0
answers
Mapping quality in Oxford Nanopore
minimap2 mapping quality oxford nanopore written 18 months ago by rah • 20 • updated 16 months ago by Biostar ♦♦ 20
0
votes
0
answers
274
views
0
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Available tools that can pick up the the alignment with highest mapping quality
bam mapping quality written 20 months ago by gerrybio2010 • 0 • updated 20 months ago by WouterDeCoster ♦ 45k
5
votes
1
answer
1.2k
views
1
answer
Calculate average mapping quality at a position
mapping quality mpileup written 2.5 years ago by hpapoli • 90 • updated 2.5 years ago by Gabriel R. • 2.8k
4
votes
0
answers
4.1k
views
0
answers
BWA-mem MAPQ Calculation
mq bwa-mem mapping quality mapq alignment written 4.6 years ago by rfriedman22 • 40 • updated 2.5 years ago by h.mon ♦ 32k
0
votes
0
answers
736
views
0
answers
which indel to consider
exome mapping quality indel calls cigar value written 3.6 years ago by Kritika • 260 • updated 3.6 years ago by Pierre Lindenbaum ♦ 133k
16
votes
4
answers
7.8k
views
4
answers
How to select aligned reads below certain mapping Quality (from BWA)?
alignment samtools mapping quality bam bwa written 4.4 years ago by kirannbishwa01 • 1.3k
4
votes
0
answers
6.5k
views
0
answers
All the reads aligned using STAR have low mapping quality (0-3). What is happening?
alignment mapping quality bwa star written 4.5 years ago by kirannbishwa01 • 1.3k
1
vote
1
answer
3.2k
views
1
answer
What is the difference between the "match score", the mapping quality score under the tmap mapping pipeline
mapping quality match score tmap alignment score written 5.1 years ago by BioinfoNovice • 110 • updated 5.1 years ago by _r_am ♦ 32k
6
votes
1
answer
2.1k
views
1
answer
Why does BWA give different Mapping Quality to identical reads?
alignment mapping quality bwa written 5.7 years ago by Asdp • 40 • updated 5.7 years ago by matted ♦ 7.3k
0
votes
0
answers
2.8k
views
0
answers
Samtools : what is threshold for the mapping quality?
next-gen samtools mapping quality snp written 6.1 years ago by Govardhan Anande • 140 • updated 6.0 years ago by Biostar ♦♦ 20
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