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questions
0
votes
0
replies
213
views
Differentiate sequenced and imputed variants in BGEN files
imputation
bgen
ukb
6 months ago by
user230613
▴ 360
0
votes
0
replies
357
views
Calculating PRS from pre-computed PGS Catalog
GWAS
PRS
PGS
6 months ago by
user230613
▴ 360
10
votes
10
replies
5.6k
views
fgsea after deseq2, criteria for ranking DEGs.
GSEA
updated 23 months ago by
ATpoint
82k • written 24 months ago by
user230613
▴ 360
2
votes
6
replies
1.2k
views
lfcShrink MA plot comparison
lfcShrink
deseq2
updated 2.2 years ago by
Michael Love
★ 2.6k • written 2.2 years ago by
user230613
▴ 360
1
vote
3
replies
1.3k
views
convert CDS coordinates of a GTF to amino acid coordinates respect the resultant protein
protein coordinates
3.8 years ago by
user230613
▴ 360
9
votes
9
replies
3.7k
views
Extract sequence number "X" from multifasta file
fasta
updated 2.2 years ago by
Ram
44k • written 9.5 years ago by
user230613
▴ 360
2
votes
3
replies
5.9k
views
CIRCOS plot with Chip-Seq Data
ChIP-Seq
circos
updated 4.0 years ago by
bernatgel
★ 3.4k • written 8.8 years ago by
user230613
▴ 360
21
votes
10
replies
16k
views
9 follow
Extract reads within given region, and their mates
bam
samtools
updated 14 months ago by
dagsbio
▴ 20 • written 8.9 years ago by
user230613
▴ 360
4
votes
4
replies
5.2k
views
Does vcf-consensus support indels?
consensus
vcf-consensus
updated 6.2 years ago by
Johan Zicola
▴ 70 • written 8.2 years ago by
user230613
▴ 360
0
votes
1
reply
1.8k
views
Mate negative strand flag does not match read negative strand flag of mate
bam
validatesamfile
rnaseq
updated 6.4 years ago by
Santosh Anand
5.7k • written 6.4 years ago by
user230613
▴ 360
1
vote
1
reply
2.2k
views
consensus sequence of complex estructural variants
consensus
estructural variant
updated 2.1 years ago by
Ram
44k • written 9.3 years ago by
user230613
▴ 360
6
votes
9
replies
9.8k
views
6 follow
Intersect multiple bed and keep all fields
bed
bedtools
bedops
updated 19 months ago by
Ram
44k • written 8.8 years ago by
user230613
▴ 360
5
votes
1
reply
3.1k
views
GATK; Variant calling RNA-Seq best practices: bam processing steps
variant-calling
RNA-Seq
gatk
updated 7 months ago by
Ram
44k • written 6.7 years ago by
user230613
▴ 360
8
votes
4
replies
5.8k
views
TPM VS FPKM VS TMM and K-mer specific expression quantification
RNA-Seq
kmer
updated 6.8 years ago by
Rob
6.6k • written 7.0 years ago by
user230613
▴ 360
3
votes
4
replies
1.5k
views
Specific sequence abundance using RNA-Seq
expression
RNA-Seq
updated 6.9 years ago by
Brian Bushnell
20k • written 6.9 years ago by
user230613
▴ 360
3
votes
3
replies
2.2k
views
Subset of transcripts - Do I need to re-scale the TPM values?
RNA-Seq
tpm
kallisto
7.0 years ago by
user230613
▴ 360
7
votes
11
replies
10.0k
views
7 follow
kallisto: strand-specific and fragment length calculation
RNA-Seq
kallisto
updated 7.0 years ago by
pmelsted
▴ 120 • written 7.0 years ago by
user230613
▴ 360
1
vote
3
replies
2.5k
views
bam-readcount tool: output zero coverage bases
bam-readcount
updated 7.1 years ago by
Chris Miller
22k • written 7.1 years ago by
user230613
▴ 360
2
votes
8
replies
2.5k
views
samstat and samtools differ in the number of MAPQ=0 reads/alignments.
bwa
samtools
samstat
7.1 years ago by
user230613
▴ 360
0
votes
1
reply
2.0k
views
Varscan2 filters AND usability of the tool - looking for opinions
varscan2
variant calling
varscan
somatic
7.2 years ago by
user230613
▴ 360
5
votes
4
replies
3.9k
views
WES reads mapping: RNASeq or DNASeq aligner?
mapping
alignment
wes
updated 7.2 years ago by
cschu181
★ 2.8k • written 7.2 years ago by
user230613
▴ 360
7
votes
7
replies
6.6k
views
NGS data simulation: VarSim or BAMSurgeon?
simulation
varsim
bamsurgeon
updated 7.3 years ago by
d-cameron
★ 2.9k • written 7.3 years ago by
user230613
▴ 360
5
votes
3
replies
4.4k
views
SomaticSniper VS Varscan2
varscan2
variant-calling
somaticSniper
updated 7 months ago by
Ram
44k • written 7.3 years ago by
user230613
▴ 360
0
votes
1
reply
2.9k
views
rsem-calculate-expression prints out the help information when trying to run it
rsem
updated 7.5 years ago by
Biostar
20 • written 7.6 years ago by
user230613
▴ 360
6
votes
4
replies
3.9k
views
GFF3 ID field: "Official" nomenclature
gff3
updated 7.8 years ago by
Daniel Standage
4.1k • written 8.2 years ago by
user230613
▴ 360
1
vote
0
replies
1.8k
views
samtools mpileup -B or -E
mpileup
samtools
variant-calling
updated 7 months ago by
Ram
44k • written 8.1 years ago by
user230613
▴ 360
3
votes
4
replies
2.5k
views
Samtools: variant calling for INDELs
samtools
mpileup
updated 8.2 years ago by
Pierre Lindenbaum
162k • written 8.2 years ago by
user230613
▴ 360
1
vote
9
replies
3.7k
views
Filter blastn results by kingdom
blastn
perl
bioperl
8.4 years ago by
user230613
▴ 360
4
votes
5
replies
4.7k
views
promoter position estimation
promoter
gff3
updated 22 months ago by
Ram
44k • written 8.4 years ago by
user230613
▴ 360
15
votes
2
replies
15k
views
Trinity strand specific: RF or FR
trinity
updated 8.4 years ago by
Juke34
8.6k • written 8.4 years ago by
user230613
▴ 360
2
votes
1
reply
3.0k
views
SICER Fragment size estimation
ChIP-Seq
updated 2.0 years ago by
Ram
44k • written 8.8 years ago by
user230613
▴ 360
5
votes
13
replies
3.7k
views
From colorspace to basespace format
solid
colorspace
updated 17 months ago by
Ram
44k • written 9.0 years ago by
user230613
▴ 360
4
votes
6
replies
4.8k
views
bam processing before variant calling
variant calling
updated 23 months ago by
Ram
44k • written 9.1 years ago by
user230613
▴ 360
1
vote
3
replies
4.4k
views
ggheatmap R script error.
R
updated 24 months ago by
Ram
44k • written 9.2 years ago by
user230613
▴ 360
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