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710 results • Page
2 of 15
Sort: Votes
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Votes
Replies
4
votes
1
reply
342
views
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
limma
updated 6 days ago by
dariober
14k • written 7 days ago by
Holly
▴ 30
4
votes
6
replies
3.9k
views
Taking the difference of two VCFs (or removing singletons)
genome
sequencing
singleton
SNP
filter
updated 21 days ago by
Andres
▴ 20 • written 9.7 years ago by
hermathena
▴ 40
4
votes
2
replies
278
views
Analysis of intronic reads included scRNA-seq data
single-cell
updated 17 days ago by
Ram
44k • written 18 days ago by
carolofharvest
▴ 40
4
votes
3
replies
385
views
Kraken2 database
kraken
microbialdb
database
krakendb
kraken2
updated 8 days ago by
Mathew
▴ 150 • written 10 days ago by
Christopher
• 0
4
votes
6
replies
3.8k
views
How to interpret DEXseq results in therms of significance
DEXseq
RNA-Seq
exon
updated 15 days ago by
Sara
▴ 30 • written 6.7 years ago by
Lila M
★ 1.2k
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
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
4
votes
5
replies
3.4k
views
How to compare compare two Sam files to check mapping
alignment
updated 13 days ago by
DavidStreid
▴ 90 • written 6.4 years ago by
madhu.9124
▴ 60
4
votes
3
replies
3.0k
views
How to solve the error 'ERROR::MATE_NOT_FOUND:Found xxx unpaired mates' when run SamToFastq
samtofasq
picard
validatesamfile
updated 12 days ago by
Pierre Lindenbaum
161k • written 12 days ago by
Lila M
★ 1.2k
4
votes
4
replies
3.0k
views
CNVkit for somatic copy number detection
cnv
cnvkit
exome
WES
updated 7 days ago by
Anitha
• 0 • written 5.1 years ago by
stephaniem
• 0
4
votes
2
replies
290
views
GRCh38.gmap file
gnomix
gmap
17 days ago by
lorena9132
▴ 10
4
votes
1
reply
218
views
Extracting only 4-fold degenerate sites from gene sequences/alignments?
alignments
7 days ago by
J.
▴ 40
4
votes
11
replies
911
views
Redirection of Duplicate PMIDs
pubmed
pmid
updated 28 days ago by
LauferVA
4.2k • written 29 days ago by
dominickd
• 0
4
votes
0
replies
169
views
Herald:
The Biostar Herald for Monday, April 29, 2024
herald
22 days ago by
Biostar
2.8k
4
votes
7
replies
646
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity
scVelo
scRNA-seq
splicing
22 days ago by
e.r.zakiev
▴ 210
4
votes
7
replies
628
views
To get p-values for the TPM
P-value
TPM
RSEM
updated 26 days ago by
dsull
★ 6.0k • written 27 days ago by
VITALA
• 0
4
votes
11
replies
855
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
just now by
J
▴ 10
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
4
votes
7
replies
446
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
8 days ago by
Chen
• 0
4
votes
9
replies
513
views
Faster Needleman-Wunsch rapid global alignment of two sequences?
Needleman-Wunsch
alignment
4 days ago by
Gabriel R.
★ 2.9k
4
votes
1
reply
272
views
LD-prune variants while maintaining a list of SNPs
snp
vcf
plink
filtering
independent
updated 15 days ago by
zx8754
11k • written 17 days ago by
Jautis
▴ 560
4
votes
2
replies
293
views
How can I analyze normalized expression data?
DEseq2
RNA-seq
12 days ago by
mnx0723
• 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
4
votes
9
replies
641
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA
R
VARIANCE
updated 16 hours ago by
marco.barr
▴ 130 • written 6 days ago by
diqixiaoyaoer
▴ 20
4
votes
3
replies
447
views
Source other conda environments in a nextflow pipeline when nextflow itself is in a conda environment?
hpc
conda
nextflow
updated 24 days ago by
Arup Ghosh
3.2k • written 25 days ago by
chaco001
▴ 40
4
votes
2
replies
199
views
Duplicated sequence samtools
bowtie2
samtools
updated 8 days ago by
GenoMax
142k • written 8 days ago by
Moinuddin
• 0
4
votes
5
replies
4.4k
views
Tool:
GRIDSS: the Genomic Rearrangement IDentification Software Suite
Assembly
Structural-Variation
Variant-Calling
updated 5 days ago by
dario.garvan
▴ 520 • written 7.2 years ago by
d-cameron
★ 2.9k
3
votes
8
replies
644
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
15 days ago by
Qroid
▴ 40
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
3
votes
5
replies
427
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome
PHG
graph
11 hours ago by
beantkapoor16
▴ 10
3
votes
5
replies
366
views
Per base sequence content error in RNAseq analysis
RNA-seq
analysis
updated 29 days ago by
GenoMax
142k • written 29 days ago by
ahmad.sajad4541
• 0
3
votes
3
replies
379
views
genome assembly records not present in assembly_summary.txt
ncbi
bacteria
assembly
updated 25 days ago by
GenoMax
142k • written 25 days ago by
sapuizait
▴ 10
3
votes
3
replies
2.5k
views
How to make a TSS enrichment plot in ATAC-seq analysis?
ATAC
updated 26 days ago by
sp
• 0 • written 22 months ago by
Dan
▴ 180
3
votes
4
replies
428
views
Why gatk VariantAnnotator required bam and coverage files
gatk
VariantAnnotator
26 days ago by
QX
• 0
3
votes
3
replies
302
views
Getting the nucleotide sequence of proteins, having their UniProt IDs
Nucleotide
Genomic
Sequence
Uniprot
Proteins
updated 29 days ago by
GenoMax
142k • written 29 days ago by
Mariana
▴ 40
3
votes
5
replies
419
views
Super ehancers
enhancers
updated 6 hours ago by
jared.andrews07
★ 17k • written 19 days ago by
Oburah
• 0
3
votes
6
replies
775
views
Ciriquant not configuring hisat2 indexed files
ciriquant
29 days ago by
Atul K.
• 0
3
votes
5
replies
653
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align
RNA-Seq
linux
STAR
29 days ago by
n_navy
• 0
3
votes
3
replies
301
views
Gene Specific coverage from WGS data
WGS
SARS-CoV2
updated 8 days ago by
Ram
44k • written 21 days ago by
Adyasha
• 0
3
votes
4
replies
356
views
Truncated metadata file report from ENA Portal API
ena
python
11 days ago by
Giulia
• 0
3
votes
3
replies
761
views
KissDE and batch effect
kissDE
kissplice
29 days ago by
david.b.rombaut
▴ 10
3
votes
5
replies
425
views
Converting CRAM to FastQ
GATK
samtools
cram
SamToFastq
fastq
18 days ago by
Maverick
▴ 10
3
votes
3
replies
250
views
Getting differential ChIP-seq peaks between conditions after calling consensus peaks
MAnorm
ChIP-seq
consensus
peaks
updated 5 days ago by
ATpoint
82k • written 6 days ago by
Alexandra
• 0
3
votes
0
replies
245
views
News:
Webinar “Learning Single-cell Atlases” with Dr. Fabian Theis, author of Scanpy on May 8
Scanpy
Generative-AI
scRNA
Machine-Learning
updated 25 days ago by
Ram
44k • written 25 days ago by
Claire Watson
▴ 60
3
votes
4
replies
430
views
finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame (uORF)"
UTR
masspec
uORF
peptide
updated 5 days ago by
GenoMax
142k • written 5 days ago by
Pierre Lindenbaum
161k
3
votes
8
replies
6.6k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk
genomicsdbimport
updated 19 days ago by
Sd
• 0 • written 5.1 years ago by
Nicolas Rosewick
11k
3
votes
4
replies
494
views
Design matrix Differential expression analysis
RNA-seq
Differential-expression
updated 15 days ago by
Gordon Smyth
★ 7.2k • written 18 days ago by
SHN
▴ 40
3
votes
3
replies
321
views
How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
gatk
vcf
liftover
updated 11 days ago by
Ram
44k • written 11 days ago by
Omics data mining
▴ 260
3
votes
2
replies
291
views
imputation through beagle
panel
beagle
reference
imputation
7 days ago by
analyst
▴ 50
3
votes
6
replies
537
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 9 days ago by
Pine
▴ 20 • written 16 days ago by
snajafy
• 0
710 results • Page
2 of 15
Recent Votes
Comment: NGS forensics: how to know if data is fabricated
T2T-CHM13 "complete" human genome gff/gtf annotation file
Answer: T2T-CHM13 "complete" human genome gff/gtf annotation file
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
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Recent Replies
Comment: BiomartException: Query ERROR for existing dataset in BioMart
by
Nyksubuz
▴ 20
Could share some examples for gene_ids?
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 …
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