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questions
1
vote
2
replies
261
views
STACKS PCR duplicate removal
PCR
VCF
STACKS
RAD-seq
4 weeks ago by
maxrwjones
▴ 60
5
votes
5
replies
449
views
Including reference genome in SNP-based phylogeny
phylogeny
VCF
WGS
6 weeks ago by
maxrwjones
▴ 60
1
vote
2
replies
312
views
Phylogeny from mixed GBS and WGS
VCF
Phylogeny
GBS
WGS
tree
10 weeks ago by
maxrwjones
▴ 60
12
votes
22
replies
4.9k
views
Trimmomatic failing to cut known adapter
trimmomatic
updated 17 months ago by
Istvan Albert
100k • written 2.5 years ago by
maxrwjones
▴ 60
2
votes
2
replies
845
views
Confused by MACS2 --scale-to option
macs2
macs
ChIP
ATAC
2.5 years ago by
maxrwjones
▴ 60
0
votes
0
replies
431
views
bedtools genomecov fractions not summing to 1
genomecov
bedtools
3.0 years ago by
maxrwjones
▴ 60
3
votes
2
replies
1.9k
views
Bedtools intersect PE BAM reads
intersect
BAM
bedtools
3.0 years ago by
maxrwjones
▴ 60
2
votes
2
replies
1.2k
views
Bedtools intersect 0- and 1-based coordinate files
gff
intersect
bedtools
bam
3.0 years ago by
maxrwjones
▴ 60
6
votes
12
replies
2.7k
views
BAI index format
BAI
index
BAM
CSI
3.0 years ago by
maxrwjones
▴ 60
2
votes
2
replies
997
views
Samtools view filter by reference sequence
samtools
3.1 years ago by
maxrwjones
▴ 60
4
votes
7
replies
2.2k
views
How are BWA/bowtie/etc indices built for multiple fasta entries?
index
fasta
mapping
BWA
bowtie
3.1 years ago by
maxrwjones
▴ 60
2
votes
4
replies
1.5k
views
ATAC-seq - remove mt reads using KMC
samtools
chrM
ATAC-seq
mitochondria
KMC
3.1 years ago by
maxrwjones
▴ 60
0
votes
2
replies
922
views
How can a duplicate read be interchromosomal?
interchromosomal
duplicate
NGS
samtools
picard
3.1 years ago by
maxrwjones
▴ 60
4
votes
5
replies
1.9k
views
Bowtie2 & Hisat2 SAM flags above 256?
manual
SAM
read-mapping
flags
bowtie2
3.1 years ago by
maxrwjones
▴ 60
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