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711 results • Page
2 of 15
Sort: Views
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Views
Votes
Replies
0
votes
6
replies
2.1k
views
Copy number Variation analysis using conumee
R
software error
sequencing
genome
updated 12 days ago by
GenoMax
142k • written 3.2 years ago by
gs000095
▴ 10
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference
38build
impute
imputation
22 days ago by
anna
▴ 20
3
votes
6
replies
2.0k
views
7 follow
DNA methylation preprocessing
SWAN
DNA
methylation
Funnorm
updated 25 days ago by
Ram
44k • written 2.4 years ago by
SYOSY
▴ 10
2
votes
6
replies
1.9k
views
How can you *consistently* download BioProject IDs from NCBI's BioSample database using Entrez Direct?
XML
ncbi
entrez-direct
updated 6 days ago by
Ram
44k • written 3.9 years ago by
millere
• 0
6
votes
6
replies
1.8k
views
agilent human all exon sureselct v7 bed file
exon
human
bed
v7
agilent
all
sureselect
updated 16 days ago by
MiladAD
▴ 10 • written 2.0 years ago by
soheil
• 0
2
votes
2
replies
1.8k
views
Parametric or non-parametric tests for qPCR significance testing between treatments?
qPCR
statistical test
parametric
non-parametric
updated 18 days ago by
e.r.zakiev
▴ 210 • written 3.9 years ago by
n.anuragsharma
▴ 40
0
votes
3
replies
1.7k
views
Running STRUCTURE from command line
STRUCTURE
updated 4 hours ago by
Ram
44k • written 3.0 years ago by
giulia.trauzzi
▴ 10
6
votes
5
replies
1.7k
views
How to calculate coverage of Nanopore long read data?
sequencing
coverage
6 days ago by
Arton
▴ 10
1
vote
2
replies
1.7k
views
Seurat CellCycleScoring – confused about the proper order of operations when using SCTransform
CellCycleScoring
SCTransform
Seurat
updated 12 days ago by
Li
• 0 • written 2.3 years ago by
GPM
▴ 10
4
votes
15
replies
1.7k
views
how to test for differential expression in samples where a global increase in gene expression is expected
edgeR
DESeq
Differential-Expression
RNA-Seq
updated 17 days ago by
Gordon Smyth
★ 7.2k • written 5 months ago by
raplayer
▴ 10
0
votes
9
replies
1.5k
views
kinannote software installation problems
kinannote
updated 13 days ago by
Emanoelle
• 0 • written 5.8 years ago by
Elizabeth
▴ 30
1
vote
6
replies
1.5k
views
CellRanger output more cells than specified using --force-cells? Why?
scRNA-seq
cellranger
updated 2 days ago by
scideas
▴ 30 • written 8 months ago by
rohitsatyam102
▴ 870
2
votes
7
replies
1.4k
views
6 follow
Differential Expression using Isoseq-supplemented reference transcriptome
RNA-Seq
Salmon
Isoseq
updated 22 days ago by
Gordon Smyth
★ 7.2k • written 8 months ago by
Calum
▴ 10
1
vote
2
replies
1.3k
views
Extracting named fasta sequences according to list with Biopython
Biopython
FASTA
updated 8 days ago by
Rubayetul
• 0 • written 2.6 years ago by
lachiemck
• 0
8
votes
16
replies
1.2k
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 25 days ago by
bk11
★ 2.5k • written 10 weeks ago by
Sofia
• 0
4
votes
6
replies
1.2k
views
Soft-clipping read ends based on read group
ancient
molecule
at
bam
DNA
RG
ends
clipping
damage
updated 13 days ago by
chenl
▴ 10 • written 2.5 years ago by
Martyna
• 0
1
vote
2
replies
1.2k
views
News:
The GDC Legacy Archive is retiring soon.
genomic-data-commons
tcga
gdc
16 days ago by
Zhenyu Zhang
★ 1.2k
1
vote
4
replies
1.1k
views
Filtering qscore on dorado
dorado
filtering
QC
nanopore
Guppy
19 days ago by
eebloom
▴ 80
3
votes
0
replies
1.1k
views
Tool:
Sars-Cov-2 Genome & ACE 2 Exploration
sequence
alignment
SNP
genome
16 days ago by
Ibrahim Tanyalcin
★ 1.2k
2
votes
10
replies
1.1k
views
HGVS Nomenclature of Multiple Indels found in Cis
Nomenclature
HGVS
updated 1 day ago by
Ram
44k • written 5 months ago by
LauferVA
4.2k
1
vote
10
replies
1.1k
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq
DESeq2
DNA-contamination
27 days ago by
DKA
▴ 40
2
votes
3
replies
1.1k
views
Is it possible to run CibersortX with a very small number of samples?
cibersortx
updated 6 hours ago by
finch
• 0 • written 19 months ago by
Aspire
▴ 330
2
votes
11
replies
1.0k
views
Questions about a bug when transferring cram file to bam file
sequence
samtools
bcftools
updated 22 days ago by
jkbonfield
★ 1.2k • written 4 weeks ago by
me
• 0
2
votes
3
replies
1.0k
views
Method to detect genome doubling
CNV
genome doubling
updated 29 days ago by
LauferVA
4.2k • written 4.5 years ago by
CY
▴ 750
13
votes
14
replies
1.0k
views
High Malat-1 expression in single cell data
single-cell
updated 13 days ago by
t.montserrat.ayuso
▴ 40 • written 22 days ago by
carolofharvest
▴ 40
7
votes
16
replies
986
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
22 days ago by
Ruqaiya
• 0
1
vote
8
replies
973
views
Adding CB tag to bam file
samtools
bam
updated 26 days ago by
Pierre Lindenbaum
161k • written 4 weeks ago by
Maria
• 0
2
votes
5
replies
963
views
Retrieval of Active site information programmatically
Catalytic
Python
Active
PDB
site
Site
updated 22 days ago by
Wayne
★ 2.0k • written 2.1 years ago by
arinjoy
• 0
2
votes
9
replies
960
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 27 days ago by
LauferVA
4.2k • written 7 months ago by
Gnana
• 0
4
votes
11
replies
911
views
Redirection of Duplicate PMIDs
pubmed
pmid
updated 27 days ago by
LauferVA
4.2k • written 28 days ago by
dominickd
• 0
1
vote
10
replies
910
views
error to run rnammer
phylogenomics
rRNA_extraction
rnammer
updated 15 days ago by
antonio.spl
• 0 • written 4 months ago by
microorganism_001
▴ 30
0
votes
2
replies
872
views
AGeNT LocatIt
AGeNT
LocatIt
WES
UMI
duplicates
updated 27 days ago by
barslmn
★ 2.2k • written 2.9 years ago by
jhy
▴ 10
2
votes
3
replies
872
views
Issues with Mixture file when using CIBERSORTx
Deconvolution
CIBERSORTx
updated 17 days ago by
vjanve
• 0 • written 7 months ago by
mateomejias
• 0
4
votes
10
replies
850
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 17 hours ago by
Alex Reynolds
35k • written 25 days ago by
J
▴ 10
10
votes
14
replies
830
views
6 follow
Bacterial plasmid analysis
bacteria
plasmid
wgs
hybridassembly
sequencing
updated 14 days ago by
GenoMax
142k • written 20 days ago by
nicole.kavanagh
• 0
4
votes
6
replies
822
views
7 follow
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 24 days ago by
dsull
★ 6.0k • written 28 days ago by
qudrat.nii
▴ 10
1
vote
5
replies
814
views
Converting IGV to Figure using Illustrator (or other tools)
Illustrator
IGV
written 6 months ago by
Daniel
▴ 30
1
vote
3
replies
811
views
About runing Pilon on individual chromosomes when polish draft genome assembly
Pilon
chromosome
polish
genome
draft
updated 5 days ago by
sansan_96
▴ 90 • written 2.7 years ago by
boymin2020
▴ 80
0
votes
1
reply
809
views
cnetplot category names are too long
clusterprofiler
RNA-Seq
enrichplot
cnetplot
updated 19 days ago by
Ram
44k • written 2.7 years ago by
carov
• 0
1
vote
16
replies
789
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
ncbi
updated 3 days ago by
GenoMax
142k • written 6 days ago by
hophuquy0944
• 0
0
votes
1
reply
787
views
Can I run cellassign on samples independently if there is batch effect present?
RNA-Seq
R
cellassign
batch-effect
updated 23 days ago by
Francesco
▴ 10 • written 3.4 years ago by
gt
▴ 30
8
votes
8
replies
783
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 26 days ago by
swbarnes2
14k • written 27 days ago by
Aaliya
▴ 10
0
votes
3
replies
782
views
Why cd-hit-est not work when sequence identity threshold<0.95?
genome
cluster
sequence
updated 22 days ago by
weidonglu
• 0 • written 21 months ago by
JZX
• 0
3
votes
6
replies
775
views
Ciriquant not configuring hisat2 indexed files
ciriquant
29 days ago by
Atul K.
• 0
2
votes
11
replies
770
views
DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts in whole blood: is it normal to always get NS?
rstudio
DEG
limma
4 days ago by
egascon
• 0
2
votes
9
replies
769
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 6 days ago by
Pierre Lindenbaum
161k • written 14 days ago by
schmince
• 0
3
votes
4
replies
769
views
Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (without Blat)
mapping
29 days ago by
rahu
• 0
1
vote
6
replies
763
views
anRichment is missing
WGCNA
anRichment
updated 15 days ago by
GenoMax
142k • written 6 months ago by
michael.flower.14
▴ 180
3
votes
3
replies
761
views
KissDE and batch effect
kissDE
kissplice
29 days ago by
david.b.rombaut
▴ 10
0
votes
2
replies
758
views
homer not configured properly
Homer
makeTagDirectory
updated 18 days ago by
clairechung112
• 0 • written 2.0 years ago by
amahdi779
• 0
711 results • Page
2 of 15
Recent Votes
Comment: Problem in getting geo file through GEOQUERY
Answer: Problem in getting geo file through GEOQUERY
Comment: SnpEff and Snpsift
Comment: Problem in getting geo file through GEOQUERY
Answer: Question about samtools view flags (paired reads vs. properly paired reads)
Answer: Functional enrichment analysis for unique gene IDs
Comment: Super ehancers
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Comment: Problem in getting geo file through GEOQUERY
by
anasjamshed
▴ 120
yeah but i am unable to find the link of GPL6244.soft.gz
Comment: Problem in getting geo file through GEOQUERY
by
ATpoint
82k
> Can you send me ftp link so I can download that soft file manually? Please find this link on your own by browsing the respective GEO ent…
Comment: Problem in getting geo file through GEOQUERY
by
anasjamshed
▴ 120
Thanks . I have downloaded all other files but just have problem in Error in downloadFile(myurl, destfile, mode = mode, quiet = TRUE)…
Answer: Problem in getting geo file through GEOQUERY
by
ATpoint
82k
Code runs for me and finishes in seconds. Maybe some poor internet connection on your end. Just set the timeout to 9999999 and retry. If th…
Comment: transanno liftvcf "Error: length of chromosome [chr] is not equal to length in c
by
ezz3
• 0
Thanks. I was wondering if that is the case but was having some issues understanding the transanno code which is written in rust and I don…
Answer: Multi-ploid data in ANGSD and NGSadmix
by
andersdetermig
▴ 20
1 ) I would not expect the haploid individuals to always cluster together but the model assumptions are violated. First of all the diploid…
Comment: transanno liftvcf "Error: length of chromosome [chr] is not equal to length in c
by
Pierre Lindenbaum
161k
"Are you using correct reference?" may be your reference is not using the same chrM. see https://www.biostars.org/p/199796/#199803
Comment: Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
by
shpak.max
▴ 50
Could you please elaborate on what you mean by passing -L or -V, i.e. what would the appropriate argument be for -L with UnifiedGenotyper f…
Answer: Add stats to the plot
by
Ghada
• 0
It works. I have added this code my_comparisons=list(c("HRSV", "HRSV_RBV")) plot + stat_compare_means(method = "wilcox.test",comparis…
Comment: Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
by
LChart
3.9k
I believe UnifiedGenotyper is a locus walker that sets `emitEmptySites() = False`. As such you will not see entries for positions that have…
Comment: Problem in getting geo file through GEOQUERY
by
anasjamshed
▴ 120
Basically this is my code: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") # # pkgs <- rowna…
Comment: Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
by
shpak.max
▴ 50
If that were the case, I would expect there not to be any uncalled sites in the vcf, yet there are a large number of sites with "." placeho…
Comment: Problem in getting geo file through GEOQUERY
by
bk11
★ 2.5k
It just runs fine for me with just a single line of code. library(GEOquery) GSE1145 <- getGEO("GSE1145", GSEMatrix=TRUE) …
Comment: Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
by
Dave Carlson
★ 1.7k
I can't speak to UnifiedGenotyper, as it has been many years since GATK stopped supporting it, and I have not used it in a long time. But …
Comment: Problem in getting geo file through GEOQUERY
by
anasjamshed
▴ 120
I want to get lot of files through code
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