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171 results • Page
1 of 4
Sort: Views
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Views
Votes
Replies
20
votes
17
replies
13k
views
17 follow
Best Practice On Variant Discovery For Bacteria?
updated 16 hours ago by
Ruqaiya
• 0 • written 11.9 years ago by
lh3
33k
7
votes
3
replies
13k
views
Z score in RNAseq
RNA-Seq
Zscore
updated 1 day ago by
Akash D
▴ 60 • written 6.5 years ago by
rob.costa1234
▴ 310
22
votes
15
replies
10k
views
12 follow
Alternatives To Liftover
liftover
genome
mapping
updated 1 day ago by
Thanujay S
• 0 • written 12.5 years ago by
woemler
▴ 170
19
votes
10
replies
7.4k
views
7 follow
T2T-CHM13 "complete" human genome gff/gtf annotation file
genomics
written 3.0 years ago by
noodle
▴ 590
11
votes
13
replies
6.7k
views
7 follow
log2 fold change in RNA-seq analysis
fold
log2
change
updated 1 day ago by
May Ling
• 0 • written 2.4 years ago by
wmsalsah
▴ 10
3
votes
4
replies
6.3k
views
MAUVE: No gene annotations in Genbank file alignments
software-error
MAUVE
RAST
genbank
alignment
updated 1 day ago by
pramach1
▴ 40 • written 9.8 years ago by
tptacek3050
▴ 70
13
votes
18
replies
6.2k
views
9 follow
Blastn, need help to increase speed
RNA-Seq
blastn
blast+
updated 2 days ago by
Dunois
★ 2.5k • written 3.3 years ago by
chiachoong_leong93
▴ 20
5
votes
4
replies
5.2k
views
6 follow
Classic threshold for log2 fold change in RNA-seq experiment
RNA-Seq
updated 1 day ago by
May Ling
• 0 • written 3.9 years ago by
Mozart
▴ 330
0
votes
7
replies
4.3k
views
B allele frequency (BAF)
snp
updated 6 days ago by
aidangcruickshank
▴ 10 • written 3.7 years ago by
rthapa
▴ 90
3
votes
7
replies
3.9k
views
Difference in Bismark output methylation call files and coverage files
RRBS
Bismark
DNA-methylation
updated 1 day ago by
Papyrus
★ 2.9k • written 3.9 years ago by
linelr
▴ 40
8
votes
9
replies
3.1k
views
7 follow
Venter Genome Vcf
vcf
updated 23 hours ago by
ericrkofman
▴ 20 • written 10.1 years ago by
win
▴ 980
7
votes
14
replies
2.9k
views
6 follow
How to find tandem duplications pattern in a DNA sequence
Repeat
updated 4 days ago by
micah
▴ 30 • written 3.1 years ago by
kumajis
• 0
0
votes
1
reply
2.9k
views
bfctools merge [E::hts_open_format] Failed to open file
SNP
updated 9 hours ago by
Ram
44k • written 3.6 years ago by
andemexoax
• 0
0
votes
3
replies
1.8k
views
Running STRUCTURE from command line
STRUCTURE
updated 3 days ago by
Ram
44k • written 3.0 years ago by
giulia.trauzzi
▴ 10
1
vote
6
replies
1.5k
views
CellRanger output more cells than specified using --force-cells? Why?
scRNA-seq
cellranger
updated 5 days ago by
scideas
▴ 30 • written 8 months ago by
rohitsatyam102
▴ 870
2
votes
4
replies
1.2k
views
Is it possible to run CibersortX with a very small number of samples?
cibersortx
1 day ago by
Aspire
▴ 330
2
votes
10
replies
1.1k
views
HGVS Nomenclature of Multiple Indels found in Cis
Nomenclature
HGVS
updated 4 days ago by
Ram
44k • written 5 months ago by
LauferVA
4.2k
4
votes
11
replies
938
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
2 days ago by
J
▴ 10
1
vote
3
replies
908
views
Which 1000 genomes 30x files should I use for imputation?
1000genomes
imputation
SNP
updated 1 day ago by
David-walson
• 0 • written 16 months ago by
Apprentice
▴ 160
3
votes
8
replies
874
views
Random Access remote BAM files
htslib
BAM
updated 2 days ago by
a.penatauber
• 0 • written 3 months ago by
Lucas R.F.
▴ 20
1
vote
16
replies
813
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
ncbi
updated 6 days ago by
GenoMax
142k • written 9 days ago by
hophuquy0944
• 0
1
vote
2
replies
733
views
Checking chromosome builds for genotyping data
GWAS
Liftover
PLINK
updated 5 days ago by
Muhammad
• 0 • written 2.6 years ago by
mari.johnson
• 0
4
votes
9
replies
659
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA
R
VARIANCE
updated 3 days ago by
marco.barr
▴ 130 • written 9 days ago by
diqixiaoyaoer
▴ 20
0
votes
2
replies
633
views
minfi::getQC - is default badsamplecutoff of 10.5 always appropriate? ~half of samples fail by this measure
getqc
ewas
minfi
updated 1 day ago by
June
• 0 • written 10 months ago by
rkb965
• 0
1
vote
10
replies
629
views
Add stats to the plot
R
2 days ago by
Ghada
• 0
0
votes
1
reply
610
views
Illumina methylation EPIC V2 array
ewas
methylation
enrichment
missMethyl
EPIC
updated 4 days ago by
fu_entomology
▴ 40 • written 8 months ago by
juliviglino
• 0
2
votes
7
replies
603
views
KEGG analysis in R
KEGG
clusterProfiler
Zea-mays
updated 2 days ago by
letizia.ottaviani
• 0 • written 6 weeks ago by
sansan_96
▴ 90
1
vote
10
replies
583
views
ComplexHeatmap - How to change fontsize of rowAnnotation
r
ComplexHeatmap
3 hours ago by
hannes.bongartz
• 0
1
vote
3
replies
561
views
Pruning Phylogenetic Trees and Bootstrap Values
phylogenetics
bootstrap
updated 3 days ago by
Klaus S
▴ 160 • written 6 weeks ago by
Zeng Hao
▴ 40
0
votes
8
replies
552
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp
vcf
genomics
plink
updated 5 days ago by
Pierre Lindenbaum
162k • written 14 days ago by
ajbarrett98
• 0
1
vote
8
replies
501
views
Overlapping Ranges within Granges object
Genomicranges
IRanges
GRanges
updated 6 days ago by
Alex Reynolds
35k • written 10 days ago by
ntsopoul
▴ 60
3
votes
5
replies
476
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome
PHG
graph
3 days ago by
beantkapoor16
▴ 10
3
votes
5
replies
444
views
Super ehancers
enhancers
updated 3 days ago by
jared.andrews07
★ 17k • written 22 days ago by
Oburah
• 0
3
votes
4
replies
399
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell
ambient-RNA
updated 13 hours ago by
fracarb8
★ 1.7k • written 8 days ago by
txema.heredia
▴ 130
1
vote
4
replies
396
views
some error in building kraken2 database
metagenome
kraken2
updated 1 day ago by
GenoMax
142k • written 4 weeks ago by
Art1ess
• 0
1
vote
2
replies
388
views
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
CIBERSORTx
cibersort
error
RNA-Seq
deconvolution
updated 3 days ago by
finch
• 0 • written 3 months ago by
star
▴ 10
0
votes
4
replies
382
views
How to handle duplicated genes in TCGA data?
TCGA
GDC
mRNA
updated 6 days ago by
txema.heredia
▴ 130 • written 8 days ago by
Ngrin
• 0
1
vote
6
replies
373
views
What marks a De-Novo Genome assembly as FAILED?
nanopore
denovo
illumina
assembly
genome
3 days ago by
Umer
▴ 50
0
votes
4
replies
369
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
1 day ago by
mavy
▴ 10
1
vote
2
replies
361
views
is there a tool to recover corrupted fastq files
fastq
short-read
updated 5 days ago by
Tommaso
• 0 • written 3 months ago by
pt.taklifi
▴ 60
0
votes
2
replies
359
views
transanno liftvcf "Error: length of chromosome [chr] is not equal to length in chain file. Are you using correct reference?"
liftover
transanno
3 days ago by
ezz3
• 0
1
vote
4
replies
359
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 6 days ago by
Joe
21k • written 16 days ago by
cput
• 0
0
votes
4
replies
352
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
rna-seq
5 days ago by
Bibi
• 0
2
votes
3
replies
352
views
Trimming tool
Trimming
updated 4 days ago by
Ram
44k • written 7 days ago by
GeneC
• 0
4
votes
6
replies
350
views
Mouse or Rat Gene Expression Data Similar to GTEx
whole-body
expression
atlas
1 day ago by
Shicheng Guo
★ 9.4k
3
votes
6
replies
336
views
Problem in getting geo file through GEOQUERY
geoquery
Geo
updated 2 days ago by
Ram
44k • written 3 days ago by
anasjamshed
▴ 120
0
votes
4
replies
335
views
BiomartException: Query ERROR for existing dataset in BioMart
biomart
ensembl
wheat
python
pybiomart
2 days ago by
Luqman
• 0
0
votes
2
replies
333
views
Design for complex RNA-Seq experiment using Deseq2
Model.Matrix
RNA-Seq
Limma
DESeq2
edgeR
5 days ago by
Ezequiel
• 0
0
votes
5
replies
331
views
calculating genomic coverage/ base overlap in R
genomics
updated 6 days ago by
1769mkc
★ 1.2k • written 9 days ago by
Xbox_27
• 0
1
vote
4
replies
318
views
Filtering VCF files based on VAF giving incorrect results
GATK
picard
VCF
bcftools
updated 3 days ago by
Ram
44k • written 9 days ago by
Arton
▴ 10
171 results • Page
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A: Add contig lenght to VCF header in a robust way
Answer: ComplexHeatmap - How to change fontsize of rowAnnotation
Comment: Harmony integration group.by.var parameter
Answer: Harmony integration group.by.var parameter
A: Blast - Formatting Output
Answer: Why some SNP's allele frequencies in gnomAD are so different between v2 and v4?
Comment: Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
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Comment: Introducing NovaDemux, a Sequence Demultiplexer that Increases Yield and Salvage
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> I don't know how widespread these issues are outside of JGI. Very few small/medium sequencing centers likely have NovaSeq X. This is the…
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Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
• 0
This works. Thank you so so much!
Comment: Harmony integration group.by.var parameter
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★ 17k
>I am not sure, but using "Sample_ID" might remove the differences between the conditions right ? More than likely, it'd at least impact t…
Comment: Harmony integration group.by.var parameter
by
Picasa
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Thanks jared.andrews07 for your answer. So, you are suggesting to use only "Donor" in the integration? ```r RunHarmony(seu_obj, group.by.…
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Thank you for your comment and sorry if this question might be so basic. How can I normalize the number of cells? If I am not wrong the i…
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> I want to compare the number of mutations This comparison will give you literally no useful information.
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something like: seq 1 100 4377380 | while read F ; do wget --no-check-certificate -O - "https://sorfs.ugent.be/database/micrope…
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The variability explained by the variables provided to `group.by.vars` is what Harmony will try to remove. Assuming you want to remove the …
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I think the program is trying to open a .vcf.gz.csi file rather than the actual data which is the .vcf.gz file, the csi file is not data, j…
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