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Showing :
questions
0
votes
3
replies
2.8k
views
VCF format query
vcf
updated 21 months ago by
Ram
43k • written 8.2 years ago by
AW
▴ 350
1
vote
7
replies
5.0k
views
Mpileup Segmentation Fault
mpileup
updated 5.3 years ago by
Biostar
20 • written 11.7 years ago by
AW
▴ 350
2
votes
7
replies
6.4k
views
Bowtie2 Reads that aligned concordantly exactly 1 time
Bowtie2
SAMtools
updated 15 months ago by
Ram
43k • written 9.0 years ago by
AW
▴ 350
1
vote
1
reply
2.2k
views
RSEM ignores quality scores?
RSEM
phred
6.7 years ago by
AW
▴ 350
2
votes
2
replies
5.1k
views
Cufflinks - Assigning Transcripts Or Exons
cufflinks
rna-seq
fpkm
updated 6.8 years ago by
Biostar
20 • written 11.7 years ago by
AW
▴ 350
1
vote
1
reply
2.9k
views
varscan2 mpileup2snp output contains indels
vcf
indels
mpileup2snp
varscan
updated 7.2 years ago by
Biostar
20 • written 8.2 years ago by
AW
▴ 350
0
votes
0
replies
1.4k
views
Varscan mpileup2snp coverage filter
varscan
mpileup2snp
7.5 years ago by
AW
▴ 350
0
votes
0
replies
2.9k
views
Varscan mpileup2snp parameters
varscan
mpileup2snp
snpcalling
7.5 years ago by
AW
▴ 350
0
votes
1
reply
3.1k
views
VCFtools filter - genotype quality score changes
vcftools
genotype quality
GQ
updated 7.6 years ago by
Brice Sarver
★ 3.8k • written 7.6 years ago by
AW
▴ 350
3
votes
3
replies
4.2k
views
How to do consensus calling from bam files
Consensus calling
SNPs
Samtools
BCFtools
updated 7.6 years ago by
Brice Sarver
★ 3.8k • written 7.6 years ago by
AW
▴ 350
5
votes
4
replies
4.8k
views
HISAT - Stringtie
RNA-Seq
8.0 years ago by
AW
▴ 350
0
votes
0
replies
2.6k
views
vcf format genotypes called
vcf
mpileup2snp
8.2 years ago by
AW
▴ 350
0
votes
4
replies
2.8k
views
SAM file output
sam
bowtie2
DNA-seq
updated 2.0 years ago by
Ram
43k • written 9.2 years ago by
AW
▴ 350
0
votes
2
replies
2.2k
views
Samtools mpileup vcf file
bam
vcf
SNPs
mpileup
samtools
written 8.5 years ago by
AW
▴ 350
0
votes
6
replies
3.6k
views
Extract consensus gene sequence (from gff file) from bam file
bam
DNA-seq
gff
updated 20 months ago by
Ram
43k • written 8.5 years ago by
AW
▴ 350
0
votes
6
replies
3.5k
views
samtools Mpileup quality scores?
mpileup
quality-scores
samtools
updated 20 months ago by
Ram
43k • written 8.5 years ago by
AW
▴ 350
15
votes
34
replies
12k
views
Improving efficiency of awk for large files
awk
updated 18 months ago by
Ram
43k • written 8.8 years ago by
AW
▴ 350
0
votes
4
replies
2.7k
views
SOAPdenovo assembly question
DNA-seq
SOAPdenovo
Illumina
updated 2.3 years ago by
Ram
43k • written 9.7 years ago by
AW
▴ 350
0
votes
0
replies
2.0k
views
SOAPdenovo contig parameters
genome-assembly
Illumina
SOAPdenovo2
updated 2.5 years ago by
Ram
43k • written 9.8 years ago by
AW
▴ 350
2
votes
18
replies
8.2k
views
TMM normalisation from RSEM raw counts
Rsem
RNA-seq
rpkm
TMM
EdgeR
updated 2.6 years ago by
Ram
43k • written 9.9 years ago by
AW
▴ 350
0
votes
0
replies
3.4k
views
Rsem-calculate-expression doesn't report reads processed and other stats
RSEM
RNA-Seq
updated 2.6 years ago by
Ram
43k • written 9.9 years ago by
AW
▴ 350
5
votes
2
replies
7.8k
views
EdgeR TMM normalisation
RNA-Seq
normalisation
rpkm
TMM
EdgeR
updated 2.6 years ago by
Ram
43k • written 10.0 years ago by
AW
▴ 350
12
votes
11
replies
27k
views
RNA-seq normalization: How to use TMM and rpkm() in EdgeR
normalization
RNA-Seq
RPKM
TMM
EdgeR
updated 2.6 years ago by
Ram
43k • written 10.0 years ago by
AW
▴ 350
0
votes
0
replies
2.6k
views
Tophat Both Pairs Must Map Concordantly
tophat2
updated 10.2 years ago by
Istvan Albert
100k • written 10.2 years ago by
AW
▴ 350
2
votes
3
replies
3.6k
views
Total Length Of Assembled Scaffolds Is Greater Than Genome Length
coverage
denovo
genome
assembly
updated 10.7 years ago by
ugly.betty77
★ 1.1k • written 10.7 years ago by
AW
▴ 350
0
votes
1
reply
1.9k
views
What Does The 'Readsinfofile' Option Require When Using Soapdenovo 2 With The Multikmer Method
updated 11.1 years ago by
Istvan Albert
100k • written 11.1 years ago by
AW
▴ 350
2
votes
5
replies
4.5k
views
Tophat 2 - Both Pairs Map Concordantly
tophat
paired-end
read
updated 11.7 years ago by
Istvan Albert
100k • written 11.7 years ago by
AW
▴ 350
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